Quantum-Si Inc

NOTES TO CONSOLIDATED FINANCIAL STATEMENTS

Note 1. Description of Business and Basis of Presentation

Background

Quantum-Si Incorporated (including its subsidiaries, “Quantum-Si”, “QSI”, or the “Company”) was incorporated in Delaware on June 10, 2020 as HighCape Capital Acquisition Corp. (“HighCape”). The Company’s legal name became Quantum-Si Incorporated following a business combination on June 10, 2021 between the Company and Q-SI Operations Inc. (formerly Quantum-Si Incorporated) (the “Business Combination”), which was founded in 2013.

Quantum-Si is a life sciences company focused on proteomics research, with the mission of transforming single-molecule analysis and democratizing its use by providing researchers and clinicians access to the proteome, the set of proteins expressed within a cell. The Company has developed a proprietary, universal, single-molecule detection platform that is applied to proteomics to enable next-gen protein sequencing (“NGPS”) to sequence proteins in a massively parallel fashion (rather than sequentially, one at a time), which can also be used for the study of nucleic acids. The Company believes in the ability to sequence proteins in a massively parallel fashion and offer a fast analysis time provides NGPS with the potential to unlock significant biological information through improved resolution and unbiased access to the proteome at a speed and scale not available today. Traditionally, proteomic workflows to sequence proteins required days or weeks to complete. The current platform includes the Platinum® NGPS line of instruments, Platinum Analysis Software and consumable kits for use with the Platinum line of instruments. In 2021, the Company introduced the Platinum early access program to sites with participation from leading academic centers and key industry partners. The early access program introduced the Platinum single-molecule sequencing system to key opinion leaders across the globe for both expansion and development of applications and workflows. The Company began a controlled launch of the Platinum instrument and started to take orders in December 2022, subsequently began a controlled commercial launch of Platinum in January 2023 and then moved to a full commercial launch of Platinum beginning in the second quarter of 2024. In January 2025, the Company announced the launch of the Platinum Pro benchtop sequencer. First shipments of Platinum Pro occurred in March 2025.

Liquidity and Capital Resources

The Company has historically financed its operations primarily with proceeds from the issuance of equity to private investors, as well as with the proceeds received from the closing of the Business Combination. The Company has incurred significant losses and negative cash flows from operations in all periods since inception and had an accumulated deficit of $698.0 million as of December 31, 2025. The Company has incurred significant operating losses, including net losses of $101.3 million, $101.0 million and $96.0 million for the years ended December 31, 2025, 2024 and 2023, respectively. As of December 31, 2025, the Company had cash, cash equivalents and investments in marketable securities of $215.8 million. Management believes the Company’s current cash, cash equivalents and marketable securities, together with revenue from the sales of its products and services, will be sufficient to fund its planned operations for at least the next twelve months from the date of the issuance of the accompanying Consolidated Financial Statements.

Until such time as the Company can generate significant revenue from product sales, if ever, it expects to finance its operations through private and public equity offerings, debt financings, and/or potential future collaboration, license and development agreements. However, there can be no assurance the Company will be able to complete any such transactions on acceptable terms or otherwise, and the Company may be unable to obtain sufficient additional capital when needed. The inability to raise capital as and when needed would have a negative impact on the Company’s financial condition and its ability to pursue its business strategy. The Company will need to generate significant revenue to achieve profitability and it may never do so.

Global Developments

Although the U.S. Federal Reserve lowered interest rates slightly in 2024 and in the third and fourth quarters of 2025, it is not known whether additional action will be taken to lower interest rates and if this decrease, and any other decreases, will have an impact on inflation. While these rate fluctuations have not had a significant adverse impact on the Company to date, the impact of such rate fluctuations on the overall financial markets and the economy may adversely impact the Company in the future. In addition, the global economy has experienced and is continuing to experience high levels of inflation and global supply chain disruptions. The Company continues to monitor these supply chain, inflation and interest rate factors, as well as the uncertainty resulting from the overall economic environment.

To date, the Company has not been materially affected by enacted tariffs either by the U.S. government or foreign retaliatory tariffs; however, the Company’s finished goods and/or their components could become materially affected by changing tariffs in the future. If increased tariffs are imposed on the Company’s finished goods and/or components, they may impact the business, financial condition, results of operations and cash flows.

Although the Company has not been significantly impacted by geopolitical conflicts throughout the world, the Company has experienced certain constraints in product and material availability and increasing costs required to obtain certain materials and supplies as a result of these conflicts on the global economy. To date, the business has not been materially impacted by these conflicts, however, as the conflicts continue or worsen, they may impact the business, financial condition, results of operations and cash flows.

Basis of Presentation and Principles of Consolidation

The accompanying Consolidated Financial Statements include the accounts of the Company and have been prepared in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”) and pursuant to the accounting disclosure rules and regulations of the Securities and Exchange Commission (the “SEC”). All intercompany transactions are eliminated.

Reclassifications

Certain prior year amounts have been reclassified for consistency with the current year’s presentation.

Note 2. Summary of Significant Accounting Policies

Use of Estimates

The preparation of the Consolidated Financial Statements in conformity with U.S. GAAP requires the Company to make estimates and assumptions about future events that affect the amounts recorded in its Consolidated Financial Statements and accompanying notes. Future events and their effects cannot be determined with certainty. On an ongoing basis, management evaluates these estimates and assumptions. Significant estimates and assumptions include:

•inventory valuation;

•assumptions used for leases;

•valuation of warrant liabilities;

•valuation allowances with respect to deferred tax assets;

•assumptions associated with revenue recognition; and

•assumptions underlying the fair value used in the calculation of stock-based compensation.

The Company bases these estimates on historical and anticipated results and trends and on various other assumptions the Company believes are reasonable under the circumstances, including assumptions as to future events. Changes in estimates are recorded in the period in which they become known. Actual results could differ from those estimates, and any such differences may be material to the Consolidated Financial Statements.

Concentration of Business Risk

Financial instruments that potentially subject the Company to concentration of credit risk consist principally of cash and cash equivalents and marketable securities. As of December 31, 2025 and 2024, the Company’s marketable securities consist of mutual funds, U.S. Treasury securities, U.S. government agency bonds and commercial paper. For further information regarding marketable securities, please refer to Note 3. Investments in Marketable Securities. The Company also maintains balances in certain operating accounts above federally insured limits and, as a result, the Company is exposed to credit risk in the event of default by the financial institutions to the extent account balances exceed the amount insured by the Federal Deposit Insurance Corporation.

The Company sources certain key materials and components utilized in the Company’s products from single or limited suppliers. Historically, the Company has not experienced significant issues sourcing these materials and components. However, if these suppliers were not able to supply the requested amount of materials or components, it could take a considerable length of time to obtain alternative sources, which could affect the Company’s development efforts and commercial operations.

Segment Reporting

The Company’s Chief Operating Decision Maker (the “CODM”), its Chief Executive Officer, reviews financial information presented on a consolidated basis for purposes of assessing financial performance, making operating decisions and allocating resources. Accordingly, the Company has determined that it operates as a single reportable segment. For further discussion related to segment reporting, please refer to Note 15. Segment Information.

Foreign Currency Translation and Transactions

For the Company’s international operations, the local currency has been determined to be the functional currency. The results of its non-U.S. dollar-based operations are translated to U.S. dollars at the average exchange rates during the period. Assets and liabilities are translated at the rate of exchange prevailing on the balance sheet date. Equity is translated at the prevailing rate of exchange at the date of the equity transaction. The translational effects of revaluing non-functional currency assets and liabilities were immaterial for the years ended December 31, 2025,2024 and 2023.

The Company realizes foreign currency gains/(losses) in the normal course of business based on movement in the applicable exchange rates. As of December 31, 2025 and 2024 and for the years ended December 31, 2025,2024 and 2023, the effect of foreign currency translation and transactions on the Company’s Consolidated Financial Statements wasimmaterial.

Cash and Cash Equivalents

All highly liquid investments purchased with a maturity of three months or less are classified as cash equivalents. As of December 31, 2025 and 2024, cash and cash equivalents consist of a mix of cash and short-term money market accounts, U.S. Treasury securities, U.S. government agency bonds and commercial paper.

Accounts Receivable, Net

Accounts receivable, net, is stated at the amount the Company expects to collect from customers based on their outstanding invoices. The Company reviews accounts receivable regularly to determine if any receivable may not be collectible. Such accounts receivable have been reduced by an allowance for doubtful accounts, which is our best estimate of the amount of probable credit losses in our existing accounts receivable. The Company estimates the amount of the allowance for doubtful accounts necessary to reduce accounts receivable to its estimated net realizable value by analyzing the status of significant past due receivables and current and historical bad debt trends. The Company writes off accounts receivable against the allowance when it determines a balance is uncollectible and ceases collection efforts. As of December 31, 2025 and 2024, the Company recorded an allowance against accounts receivable of $0.3 million and $0.1 million, respectively. The Company didnot write off any accounts receivable balances during the years ended December 31, 2025, 2024 and 2023.

Marketable Securities

The Company’s investments in marketable securities with original maturities of greater than three months and remaining maturities of less than one year are classified as Marketable securities, current, and investments with maturities beyond one year are classified as Marketable securities, non-current, on the Consolidated Balance Sheets.

As of December 31, 2025 and 2024 the Company’s marketable securities were classified as available-for-sale securities, carried at fair value, with the unrealized holding gains/(losses), net of income taxes, reflected in accumulated other comprehensive income/(loss) until realized. Regardless of the intent to sell a security, the Company performs additional analysis on all securities with unrealized losses to evaluate losses associated with the creditworthiness of the security. Credit losses are recorded when the Company does not expect to receive cash flows sufficient to recover the amortized cost basis of a security. For the purposes of computing realized and unrealized gains and losses, cost and fair value are determined on a specific identification basis. Purchase premiums and discounts on marketable debt securities are amortized or accreted into the cost basis over the life of the related security as adjustments to the yield using the effective-interest method.

Dividends on marketable securities are recognized as income when declared and are recorded as Dividend income in the Consolidated Statements of Operations and Comprehensive Loss. Interest income is recognized when earned.

For further discussion related to marketable securities, please refer to Note 3. Investments in Marketable Securities.

Inventory

Inventory is stated at the lower of cost or net realizable value with cost determined using the first-in, first-out method. Materials that may be utilized for either commercial or, alternatively, for research and development purposes, are classified as inventory. Amounts in inventory used for research and development purposes are charged to research and development expense when the product enters the research and development process and can no longer be used for commercial purposes and, therefore, does not have an “alternative future use” as defined in authoritative guidance.

Inventory valuation is established based on a number of factors including, but not limited to, finished goods not meeting product specifications, product excess and obsolescence, or application of the lower of cost or net realizable value concepts. The determination of events requiring the establishment of inventory valuation, together with the calculation of the amount of such adjustments may require judgment. The Company performs an assessment of the recoverability of capitalized inventory during each reporting period and, if needed, records a write-down of inventory to its estimated net realizable value in the period it is identified. For further discussion related to inventory, please refer to Note 5. Inventory.

Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets include amounts paid in advance for operating expenses as well as monies to be received from the country of France and the State of Connecticut for research and development tax credits. These research and development tax credits are exchanged for a cash refund and are typically collected within one year from the date the tax return is filed with the state. The credits are recognized as an offset to research and development expenses in the Consolidated Statements of Operations and Comprehensive Loss in the annual period the corresponding expenses were incurred.

Property and Equipment, Net

Property and equipment are stated at cost less accumulated depreciationand amortization. Depreciation expense is computed using the straight-line method over the estimated useful lives of the related assets. Leasehold improvements are amortized over the shorter of the asset’s useful life or the life of the lease term.

Estimated useful lives of property and equipment are as follows:

Expenditures for major renewals and improvements are capitalized. Expenditures for repairs and maintenance are expensed as incurred. Costs for property and equipment not yet placed into service have been recorded as construction in process and will be depreciated in accordance with the above guidelines once placed into service. When assets are retired or otherwise disposed of, the cost of these assets and related accumulated depreciation and amortization is eliminated from the balance sheet, and any resulting gains or losses are included in the Consolidated Statements of Operations and Comprehensive Loss in the period of disposal.

Capitalized Software Development Costs

The Company capitalizes certain internal use software development costs related to its SaaS platform incurred during the application development stage when management with the relevant authority authorizes and commits to the funding of the project, it is probable the project will be completed, and the software will be used as intended. The Company also capitalizes costs related to specific upgrades and enhancements when it is probable the expenditure will result in additional functionality. Costs related to preliminary project activities and to post-implementation activities are expensed as incurred.

Internal use software is amortized on a straight-line basis over its estimated useful life, which is generallytwo years. Management evaluates the useful lives of these assets on an annual basis and tests for impairment whenever events or changes in circumstances occur that could impact the recoverability of the assets. Capitalized costs are recorded as Internally developed software on the Consolidated Balance Sheets. Amortization expense related to internally developed software was $0.6 million and $0.2 million for the years ended December 31, 2024 and 2023, respectively. As of December 31, 2024, the Company’s capitalized software was fully amortized and there wasno such amortization expense for the year ended December 31, 2025.

Impairment of Long-Lived Assets

The Company reviews its long-lived assets for impairment when the Company determines a triggering event has occurred. When a triggering event has occurred, each impairment test is based on a comparison of the future expected undiscounted cash flows to the recorded value of the asset. If the recorded value of the asset is less than the undiscounted cash flows, the asset is written down to its estimated fair value. No impairments were recorded for the years ended December 31, 2025, 2024 and 2023.

Leases

The company currently leases executive office space in Branford, Connecticut, office, laboratory and manufacturing space in San Diego, California and semiconductor chip assembly and packaging space in Garnet Valley, Pennsylvania. The Company’s current leases expire at various dates through 2029.

The Company’s real estate lease agreements may include options to either renew and/or early terminate the lease. Leases with renewal options allow the Company to extend the lease term typically between 1 and 5 years. When it is reasonably certain that the Company will exercise an option to renew or terminate a lease, these options are considered in determining the classification and measurement of the lease at lease commencement.

The Company’s leases generally do not have a readily determinable implicit discount rate. As such, the Company uses an incremental borrowing rate based on the information available at the lease commencement date to determine the present value of the lease payments. The Company’s incremental borrowing rate is the estimated rate that would be required to pay for a collateralized borrowing equal to the total lease payment over the lease term. The Company measures right-of-use (“ROU”) assets based on the corresponding lease liability adjusted for (i) payments made to the lessor at or before the commencement date, (ii) initial direct costs incurred and (iii) tenant incentives under the lease. The Company’s lease terms may include options to extend or terminate the lease when it is reasonably certain it will exercise that option. Lease expense for minimum lease payments is recognized on a straight-line basis over the lease term for operating leases. Finance leases will result in a front-loaded expense pattern. With respect to finance leases, amortization of the ROU asset is presented separately from interest expense related to the finance lease liability. In addition, the Company does not have significant residual value guarantees or restrictive covenants in the lease portfolio.

Certain of the Company’s lease agreements contain tenant improvement incentives and allowances, rent holidays, or rent escalation clauses. For tenant improvement incentives, if the incentive is determined to be a leasehold improvement owned by the lessee and the Company is reasonably certain to use the incentive, the Company generally records the incentive as a reduction to the fixed lease payments liability as a reduction to lease cost. Reimbursable construction costs incurred are recorded as leasehold improvements and are amortized over the term of the lease. The Company records rental expense related to rent holidays and rent escalation clauses on a straight-line basis over the term of the lease. The Company uses the date of initial possession as the commencement date for lease incentives, which is generally when the Company is given right of access to the space and begins to make improvements in preparation for intended use.

Upon inception, leases are evaluated and classified as operating or finance for financial reporting purposes. Operating leases that are short term in nature and have month-to-month payment terms are expensed as incurred in Research and development expenses or in Selling, general and administrative expenses in the Consolidated Statements of Operations and Comprehensive Loss. The Company’s lease agreements contain variable lease costs for common area maintenance, utilities, taxes and insurance, which are expensed as incurred.

Warrant Liabilities

The Company’s outstanding warrants include publicly traded warrants (the “Public Warrants”) which were issued as one-third of one redeemable warrant per unit issued during HighCape’s initial public offering on September 9, 2020, and warrants sold in a private placement (the “Private Warrants”) to HighCape’s sponsor, HighCape Capital Acquisition LLC (the “Sponsor”). The Public Warrants and Private Warrants meet the definition of a derivative and the Company recorded these warrants as long-term liabilities on the Consolidated Balance Sheets at fair value upon the closing of the Business Combination, with subsequent changes in their respective fair values recognized in the Consolidated Statements of Operations and Comprehensive Loss at each reporting date. As of December 31, 2025, the warrants are classified as current liabilities on the Consolidated Balance Sheets. For further discussion related to the Public Warrants and Private Warrants, please refer to Note 11. Warrant Liabilities.

Warranty

The Company provides a freeone-year assurance-type warranty to customers with the initial purchase of a Platinum instrument. The cost of the warranty is accrued upon the initial sale of an instrument in Accrued expenses and other current liabilities on the Consolidated Balance Sheets.

Revenue Recognition

The Company’s revenue is derived from sales of products and services. Product revenue is primarily generated from the sales of instruments and consumables used in protein sequencing and analysis. Service revenue is primarily generated from service maintenance contracts including access to analysis software and advanced training for instrument use. The Company recognizes revenue when or as a customer obtains control of the promised goods and services. The amount of revenue recognized reflects the consideration to which the Company expects to be entitled in exchange for these goods and services. This process involves identifying the contract with a customer, determining the performance obligations in the contract, determining the contract price, allocating the contract price to the distinct performance obligations in the contract, and recognizing revenue as the performance obligations have been satisfied. The Company has made the accounting policy election allowed for under ASC 606-10-32-2A to exclude all sales taxes from transaction price. Revenue recognition for contracts with multiple deliverables is based on the separate satisfaction of each distinct performance obligation within the contract. A performance obligation is considered distinct from other obligations in a contract when it provides a benefit to the customer either on its own or together with other resources readily available to the customer and is separately identified in the contract. The Company allocates transaction price to the performance obligations in a contract with a customer based on the relative standalone selling price of each performance obligation. The Company determines standalone selling price based on the price at which the performance obligation is sold separately. If the standalone selling price is not observable through past transactions, the Company estimates the standalone selling price taking into account available information and specific factors such as competitive positioning, internal costs, profit objectives, and internally approved pricing guidelines related to the performance obligation.

The Company considers performance obligation for sales of products satisfied upon shipment of the goods to the customer in accordance with the shipping terms (either upon shipment or delivery), which is when control of the product is deemed to be transferred; this includes instruments and consumables. Customers generally do not have a right to return products, except for defective or damaged products during the warranty period or unless prior written consent is provided. In instances where right of payment or transfer of title is contingent upon the customer’s acceptance of the product, revenue is deferred until all acceptance criteria have been met. Revenues for service maintenance contracts, which start after the first year of purchase and are considered as service type warranties that effectively extend the standard first-year service coverage at the customer’s option are recognized ratably over the contract service period as these services are performed evenly over time. Revenues for advanced training is recognized at a point in time upon satisfaction of the underlying performance obligation. The Company typically provides a standardone-year warranty which covers defects in materials, workmanship and manufacturing or performance conditions under normal use and service. The first year of the warranty of the products is considered an assurance-type warranty and is recorded as Cost of revenue within the Consolidated Statements of Operations and Comprehensive Loss. The Company has determined the standard first-year warranty is not a distinct performance obligation.

The Company disaggregates revenue from contracts with customers by type of revenue. The Company believes product revenue and service revenue aggregate the payor types by nature, amount, timing and uncertainty of its revenue streams. For further discussion on the disaggregation of revenue, please refer to Note 15. Segment Information.

Deferred Revenue

Deferred revenue primarily consists of billings and payments received in advance of revenue recognition from service maintenance contracts including software subscription and advanced training, and is reduced as the revenue recognition criteria are met. Deferred revenue also includes advanced training provided to customers until the service has been performed. Deferred revenue that will be recognized as revenue within the succeeding 12-month period is recorded as current and is included within Accrued expenses and other current liabilities in the Company’s Consolidated Balance Sheets. The portion of deferred revenue where revenue is expected to be recognized beyond twelve months from the reporting date is recorded as non-current deferred revenue and is included in Other long-term liabilities in the Company’s Consolidated Balance Sheets.

As of December 31, 2025, the Company had deferred revenue of $0.1 million included within Accrued expenses and other current liabilities in the Company’s Consolidated Balance Sheets. As of December 31, 2025, amounts included within Other long-term liabilities in the Company’s Consolidated Balance Sheets were immaterial. The Company expects to recognize approximately 80% of its remaining performance obligations as revenue during the year ending December 31, 2026.

Shipping and Handling Costs

Shipping and handling costs associated with outbound freight after control of a product has transferred to a customer are accounted for as fulfillment costs and are included in Cost of revenue in the Consolidated Statements of Operations and Comprehensive Loss. Shipping and handling costs billed to customers are considered part of the transaction price and are recognized as revenue with the underlying product sales.

Research and Development

Research and development expenses primarily consist of personnel costs and benefits, stock-based compensation, lab supplies, consulting and professional services, fabrication services, facilities costs, software, and other outsourced expenses. Research and development expenses are expensed as incurred and are primarily related to the development of new products and services.

Selling, General and Administrative

Selling, general and administrative expenses primarily consist of personnel costs and benefits, stock-based compensation, patent and filing fees, consulting and professional services, legal and accounting services, facilities costs, depreciation and amortization expense, insurance and office expenses, product advertising and marketing. Advertising costs are expensed as incurred. Advertising expenses were immaterial for the years ended December 31, 2025, 2024 and 2023.

Net Loss per Share

Basic net loss per share is computed by dividing the net loss attributable to common stockholders by the weighted-average number of shares of Class A and Class B common stock of the Company outstanding during the period, without consideration of potentially dilutive securities.

Diluted net loss per share is computed by dividing the net loss attributable to common stockholders by the weighted average number of Class A and Class B common shares plus the common equivalent shares of the period, including any dilutive effect from such shares. The Company’s diluted net loss per share is the same as basic net loss per share for all periods presented, since the effect of potentially dilutive securities is anti-dilutive. For further discussion, please refer to Note 12. Net Loss Per Share.

Stock-Based Compensation

Stock-based compensation expense for restricted stock and stock option grants with only service conditions is recognized on a straight-line basis over the requisite service period of the individual grants, which is generally the vesting period, based on the estimated grant date fair values. Stock-based compensation expense for stock option grants subject to non- financing event performance conditions on an accelerated basis is recognized as though each vesting portion of the award was, in substance, a separate award.

The fair value of restricted stock is estimated using the current market price of the Company’s common stock on the date of grant.

The Company measures compensation expense for stock-based awards to employees, non-employees and directors based upon the awards’ initial grant-date fair values. Stock-based compensation expense for stock options, restricted stock units and performance awards is recorded over the requisite service period. For awards with only a service condition, the Company expenses stock-based compensation using the straight-line method over the requisite service period for the entire award. For awards with a market condition, the Company expenses the grant date fair value at the target over the vesting period regardless of the value the award recipients ultimately receive. The fair value of restricted stock without a market condition is estimated using the current market price of the Company’s common stock on the date of grant. The fair value of stock option grants with a market condition is estimated at the date of grant using the Monte Carlo simulation model (“Monte Carlo”). The fair values of stock option grants with only a service condition are estimated as of the date of grant by applying the Black-Scholes option valuation model (“Black-Scholes model”). The Black-Scholes model and Monte Carlo models incorporate assumptions as to stock price volatility, the expected life of options or restricted stock, a risk-free interest rate and dividend yield. The effect of forfeiture in compensation costs is recognized based on actual forfeitures when they occur.

The Black-Scholes model is affected by the stock price on the date of the grant as well as assumptions regarding a number of variables. These variables include the expected term of the option, expected risk-free interest rate, the expected volatility of common stock, and expected dividend yield; each of which is described below. The assumptions for expected term of the option and expected volatility of common stock are the two assumptions that significantly affect the grant date fair value.

•Expected Term: The expected term is calculated using the weighted-average period that the stock options are expected to be outstanding prior to being exercised. The Company determines expected term based on historical exercise patterns and its expectation of the time it will take for employees to exercise options still outstanding. The Company estimates non-employees’ options based on the contractual term.

•Risk-free Interest Rate: The risk-free interest rate for periods within the expected term of the awards is based on the U.S. Treasury yield curve in effect at the time of the grant.

•Expected Stock Price Volatility: The Company determined expected annual equity volatility based on the combination of the historical volatility of its common stock and the historical volatility of the common stock comparable to the Company’s common stock.

•Dividend Yield: Because the Company has never paid a dividend and does not expect to begin doing so in the foreseeable future, the Company assumesno dividend yield in valuing the stock-based awards.

•Exercise Price: The exercise price is taken directly from the grant notice issued to employees and non-employees.

Income Taxes

The Company utilizes the asset and liability method of accounting for income taxes. Under this method, deferred tax assets and liabilities are recognized for the expected future tax consequences of temporary differences between the carrying amounts and the tax basis of assets and liabilities using the enacted statutory tax rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled. A valuation allowance is established against net deferred tax assets if, based on the weight of available evidence, it is more likely than not some or all of the net deferred tax assets will not be realized.

The Company accounts for uncertainty in income taxes recognized in the financial statements by applying a two-step process to determine the amount of tax benefit to be recognized. First, the tax position must be evaluated to determine the likelihood it will be sustained upon external examination by the taxing authorities. If the tax position is deemed more-likely-than-not-to be sustained, the tax position is then assessed to determine the amount of benefit to recognize in the financial statements. The amount of the benefit that may be recognized is the largest amount that has a greater than 50% likelihood of being realized upon ultimate settlement. The provision for income taxes includes the effects of any resulting tax reserves or unrecognized tax benefits that are considered appropriate, as well as the related net interest and penalties, as applicable. As of both December 31, 2025 and 2024, no accrued interest and penalties associated with any uncertain tax positions were recorded on the Consolidated Balance Sheets. The Company recognized animmaterial amount of interest and penalties in the Statements of Operations and Comprehensive Income for the year ended December 31, 2024. There wereno interest and penalties recognized in the Statements of Operations and Comprehensive Income for the years ended December 31, 2025 and December 31, 2023.

Recently Issued Accounting Pronouncements

In July 2025, the FASB issued ASU 2025-05, Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses for Accounts Receivable and Contract Assets. This standard provides entities with a practical expedient when calculating current expected credit loss by assuming the current conditions as of the balance sheet date will not change for the remaining life of the asset. The ASU is effective for fiscal years beginning after December 15, 2025 and interim periods within those annual periods, with early adoption permitted. The ASU is to be applied on a prospective basis. The Company adopted ASU 2025-05 effective January 1, 2026. The adoption of ASU 2025-05 did not have a material impact to the Consolidated Financial Statements and disclosures.

In November 2024, the FASB issued ASU No. 2024-03, Disaggregation of Income Statement Expenses (“DISE”), which requires additional disclosure of the nature of expenses included in the income statement. The ASU requires disclosures about specific types of expenses included in the expense captions presented on the face of the income statement as well as disclosures about selling expenses. The amendments in this update are effective for annual reporting periods beginning after December 15, 2026 and interim reporting periods beginning after December 15, 2027, with early adoption permitted. The ASU is required to be applied prospectively with the option for retrospective application. The Company is currently evaluating the impact ASU 2024-03 may have on its Consolidated Financial Statements and disclosures.

In March 2024, the FASB issued ASU No. 2024-02, Codification Improvements - Amendments to Remove References to the Concepts Statements, which contains amendments to the Codification that remove references to various Concepts Statements. The amendments in ASU 2024-02 are not intended to result in significant accounting changes for most entities. The Company adopted ASU 2024-02 effective January 1, 2025. The adoption of ASU 2024-02 did not have a material impact to the Consolidated Financial Statements and disclosures.

In December 2023, the FASB issued ASU No. 2023-09, Income Taxes (Topic 740): Improvements to Income Tax Disclosures, which expands income tax disclosure requirements to include additional information related to the rate reconciliation of effective tax rates to statutory rates, as well as additional disaggregation of taxes paid in both U.S. and foreign jurisdictions. The amendments in ASU 2023-09 also remove disclosures related to certain unrecognized tax benefits and deferred taxes. The Company adopted ASU 2023-09 prospectively during the year ended December 31, 2025. The impact of ASU 2023-09 was not material to the Company’s Consolidated Financial Statements. For further details regarding the Company’s income taxes, please refer to Note 14. Income Taxes.

Note 3. Investments in Marketable Securities

As of December 31, 2025 and 2024 the Company’s marketable securities were classified as available-for-sale securities, carried at fair value, with the unrealized holding gains/(losses), net of income taxes, reflected in accumulated other comprehensive income/(loss) until realized.

During the year ended December 31, 2023, the Company’s investments in marketable securities were classified as trading securities and consisted of ownership interests in fixed income mutual funds. In thefourth quarter of 2023, these trading securities were sold and the Company reinvested the funds received from the sale in marketable securities deemed to be available-for-sale securities. Unrealized gain (loss) on trading securities and realized loss on trading securities related to the Company’s trading securities for the years ended December 31, 2025, 2024 and 2023 were as follows (in thousands):

The following is a summary of the Company’s available-for-sale securities recorded within Marketable securities on the Consolidated Balance Sheets as of December 31, 2025 and 2024(in thousands):

The fair values of the Company’s available-for-sale securities included within Marketable securities on the Consolidated Balance Sheets as of December 31, 2025 and 2024, by remaining contractual maturity, are as follows (in thousands):

Note 4. Fair Value of Financial Instruments

Fair value estimates of financial instruments are made at a specific point in time, based on relevant information about financial markets and specific financial instruments. As these estimates are subjective in nature, involving uncertainties and matters of significant judgment, they cannot be determined with precision. Changes in assumptions can significantly affect estimated fair value.

The Company measures fair value as the price that would be received to sell an asset or paid to transfer a liability (an exit price) in an orderly transaction between market participants at the reporting date. The Company utilizes a three-tier hierarchy, which prioritizes the inputs used in the valuation methodologies in measuring fair value:

•Level 1: Valuations based on quoted prices in active markets for identical assets or liabilities that an entity has the ability to access.

•Level 2: Valuations based on quoted prices for similar assets or liabilities, quoted prices for identical assets or liabilities in markets that are not active, or other inputs that are observable or can be corroborated by observable data for substantially the full term of the assets or liabilities.

•Level 3: Valuations based on inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.

The carrying value of cash and cash equivalents, accounts payable and accrued expenses and other current liabilities approximates their fair values due to the short-term or on demand nature of these instruments. As of December 31, 2025 and 2024, the Company’s investment portfolio included available-for-sale securities which were comprised of money market funds, U.S. Treasury bills, U.S. government agency bonds and/or commercial paper. The Company has certain U.S. Treasury bills, U.S. government agency bonds, and commercial papers classified as Level 2 due to the fair value for these instruments being determined by utilizing observable inputs in similar assets or identical assets in non-active markets.

Warrants are recorded as Warrant liabilities, current, and Warrant liabilities, non-current, on the Consolidated Balance Sheets as of December 31, 2025 and December 31, 2024, respectively. The warrant liabilities are measured at fair value at inception and on a recurring basis, with changes in fair value presented as Change in fair value of warrant liabilities in the Consolidated Statements of Operations and Comprehensive Loss.

The Public Warrants and Private Warrants were carried at fair value as of December 31, 2025 and 2024. The Public Warrants were valued using Level 1 inputs as they are traded in an active market. The Private Warrants were valued using a binomial lattice model, which results in a Level 3 fair value measurement. The primary unobservable input utilized in determining the fair value of the Private Warrants was the expected volatility of the Company’s Class A common stock. The expected volatility was based on consideration of the implied volatility from the Company’s own public warrant pricing and on the historical volatility observed at guideline public companies. As of December 31, 2025, the significant assumptions used in preparing the binomial lattice model for valuing the Private Warrants liability include (i) volatility of 263.6%, (ii) risk-free interest rate of 3.60%, (iii) strike price of $11.50, (iv) fair value of common stock of $1.10, and (v) expected life of 0.4 years. As of December 31, 2024, the significant assumptions used in preparing the binomial lattice model for valuing the Private Warrants liability include (i) volatility of 194.3%, (ii) risk-free interest rate of 4.20%, (iii) strike price of $11.50, (iv) fair value of common stock of $2.70, and (v) expected life of 1.4 years.

The following tables set forth the Company’s fair value hierarchy for assets and liabilities measured at fair value as of December 31, 2025 and 2024 (in thousands):

There were no transfers of financial assets or liabilities into or out of Level 3 for the years ended December 31, 2025 and 2024.

Note 5. Inventory

Inventory consists of the following as of December 31, 2025 and 2024 (in thousands):

Charges recorded for inventory write-downs included in Research and development expenses in the Consolidated Statements of Operations and Comprehensive Loss were $1.6 million, $3.2 million and $3.4 million for the years ended December 31, 2025, 2024 and 2023, respectively.

Charges recorded for inventory write-downs included in Cost of revenue in the Consolidated Statements of Operations and Comprehensive Loss were $0.7 million and $0.2 million for the years ended December 31, 2025 and 2024, respectively. Charges recorded for inventory write-downs included in Cost of revenue in the Consolidated Statements of Operations and Comprehensive Loss were immaterial for the year ended December 31, 2023.

Note 6. Property and Equipment, Net

Property and equipment, net, consists of the following as of December 31, 2025 and 2024 (in thousands):

Depreciation and amortization expense is included within Cost of revenue, Research and development and Selling, general and administrative expenses in the Consolidated Statements of Operations and Comprehensive Loss. For the years ended December 31, 2025, 2024 and 2023, depreciation and amortization expense was $4.5 million, $4.6 million and $4.2 million, respectively.

For the year ended December 31, 2025, the Company recorded immaterial losses on disposals relating to property and equipment of $0.1 million with accumulated depreciation and amortization of $0.1 million. For the year ended December 31, 2024, the Company recorded losses on disposals of $0.4 million relating to property and equipment of $3.2 million with accumulated depreciation and amortization of $2.8 million. For the year ended December 31, 2023, the Company recorded losses on disposals of $0.1 million relating to property and equipment of $0.3 million with accumulated depreciation and amortization of $0.2 million.

Note 7. Leases

Lease-related costs for the years ended December 31, 2025, 2024 and 2023 are as follows (in thousands):

As of December 31, 2025, the maturities of the operating lease liabilities and a reconciliation to the present value of lease liabilities were as follows (dollars in thousands):

The following table provides certain cash flow and supplemental cash flow information related to the Company’s right-of-use assets and lease liabilities for the years ended December 31, 2025 and 2024 (in thousands):

(1)The year ended December 31, 2024 includes an increase in right-of-use assets due to the change in estimated timing of receipt of reimbursements for tenant improvements related to the New Haven, Connecticut lease.

During the year ended December 31, 2025, the Company entered into the Mutual Release Agreement to terminate the lease of 67,000 square feet of space in New Haven, Connecticut, resulting in the derecognition of the right-of-use asset in the amount of $7.3 million and the related lease liability in the amount of $5.6 million which were included in Operating lease right-of-use assets and Operating lease liabilities, respectively, on the Consolidated Balance Sheets. For further details regarding this lease termination, please refer to Note 17. Commitments and Contingencies.

Note 8. Accrued Expenses and Other Current Liabilities

Accrued expenses and other current liabilities consist of the following as of December 31, 2025 and 2024 (in thousands):

Note 9. Equity Transactions

Class A Common Stock

As of December 31, 2025 and 2024, the Company had authorized 600,000,000 shares of Class A common stock at $0.0001 par value per share, of which a total of 196,431,273 and 146,953,271 shares were outstanding, respectively.

Voting Rights

Holders of Class A common stock will be entitled to castone vote per Class A share. Generally, holders of all classes of common stock vote together as a single class, and an action is approved by stockholders if a majority of votes cast affirmatively or negatively on the action are cast in favor of the action, while directors are elected by a plurality of the votes cast. Holders of Class A common stock will not be entitled to cumulate their votes in the election of directors.

Class B Common Stock

As of December 31, 2025 and 2024, the Company had authorized 27,000,000 shares of Class B common stock at $0.0001 par value per share, of which a total of 19,937,500 shares were outstanding for both years.

Voting Rights

Holders of Class B common stock will be entitled to cast 20 votes per share of Class B common stock. Generally, holders of all classes of common stock vote together as a single class, and an action is approved by stockholders if a majority of votes cast affirmatively or negatively on the action are cast in favor of the action, while directors are elected by a plurality of the votes cast. Holders of Class B common stock will not be entitled to cumulate their votes in the election of directors.

Dividend Rights of Class A and Class B Common Stock

With limited exceptions in the case of certain stock dividends or disparate dividends approved by the affirmative vote of the holders of a majority of the Class A common stock and Class B common stock, each voting separately as a class, holders of Class B common stock will share ratably (based on the number of shares of Class B common stock held), together with each holder of Class A common stock, if and when any dividend is declared by the Board out of funds legally available therefor, subject to restrictions, whether statutory or contractual (including with respect to any outstanding indebtedness), on the declaration and payment of dividends and to any restrictions on the payment of dividends imposed by the terms of any outstanding preferred stock or any class or series of stock having a preference over, or the right to participate with, the Class B common stock with respect to the payment of dividends.

Preferred Stock

As of December 31, 2025 and 2024, the Company had authorized 1,000,000 shares of preferred stock at $0.0001 par value per share. There wereno preferred shares outstanding for both years.

Preferred stock may be issued from time to time in one or more series. Any shares of preferred stock which may be redeemed, purchased or acquired by the Company may be reissued except as otherwise provided by law.

At-the-Market Equity Offering Programs

The Company filed a universal shelf registration statement on Form S-3 and a subsequent amendment to the Form S-3 (the “2025 Shelf Registration Statement”), on September 26, 2025 and October 9, 2025, respectively, covering the offering of Class A common stock, preferred stock, debt securities, warrants, rights and units. The 2025 Shelf Registration Statement replaced an equivalent shelf registration statement on Form S-3 originally declared effective on August 22, 2023 (the“2023 Shelf Registration Statement”).

On September 26, 2025, the Company entered into a Sales Agreement (the “Leerink Sales Agreement”) with Leerink Partners LLC (“Leerink”), pursuant to which the Company may offer and sell shares of its Class A common stock, having an aggregate offering price of up to $100.0 million, from time to time through an “at-the-market” offering program under which Leerink will act as sales agent (the “2025 ATM Offering”). The Company has no obligation to sell any shares under the Leerink Sales Agreement and may at any time suspend solicitation and offers under the Leerink Sales Agreement. The

2025 ATM Offering is being made pursuant to the 2025 Shelf Registration Statement and a sales agreement prospectus related to the 2025 ATM Offering. During the year ended December 31, 2025, there wereno shares sold under the Sales Agreement.

On December 11, 2024, the Company entered into an Equity Distribution Agreement (the “Canaccord Sales Agreement”) with Canaccord Genuity LLC (“Canaccord”) to sell shares of its Class A common stock having an aggregate offering price of up to $75.0 million, from time to time through an “at-the-market” offering program under which Canaccord acted as sales agent (the “2024 ATM Offering”). The Company had no obligation to sell any shares under the Canaccord Sales Agreement and could at any time suspend solicitation and offers under the Canaccord Sales Agreement. The 2024 ATM Offering was made pursuant to the 2023 Shelf Registration Statement and a prospectus supplement related to the 2024 ATM Offering dated December 11, 2024. During the year ended December 31, 2024, we sold and issued 23,425,650 shares of our Class A common stock under the 2024 ATM Offering, resulting in gross proceeds of $36.2 million. Net proceeds were $34.8 million after commissions and issuance costs of $1.4 million. The Company soldno shares of our Class A common stock under the 2024 ATM Offering during the years ended December 31, 2025 and December 31, 2023. In connection with the July 2025 Registered Direct Offering, as described below, the Company provided written notice, effective as of July 3, 2025, to Canaccord of its election to terminate the Canaccord Sales Agreement for its at-the-market offering.

Registered Direct Offerings and Pre-funded Warrants

On July 3, 2025, the Company entered into a securities purchase agreement with a certain institutional investor pursuant to which the Company agreed to issue and sell, in a registered direct offering (the “July 2025 Registered Direct Offering”), an aggregate of (i)18,200,000 shares of the Company’s Class A common stock at a price of $1.67 per share and (ii) pre-funded warrants to purchase 11,740,119 shares of common stock (the “Pre-Funded Warrants”). The Pre-Funded Warrants were exercised in full on August 1, 2025 at the exercise price of $0.0001 for one share of Class A common stock per Pre-Funded Warrant. The gross proceeds to the Company from the July 2025 Registered Direct Offering were approximately $50.0 million. After deducting estimated placement agents’ fees and other offering expenses payable by the Company, net proceeds as of December 31, 2025 were approximately $46.7 million.

On January 3, 2025, the Company entered into a securities purchase agreement with certain institutional investors pursuant to which the Company agreed to issue and sell, in a registered direct offering (the “January 2025 Registered Direct Offering”) an aggregate of 15,625,000 shares of the Company’s Class A common stock at a price of $3.20 per share. The gross proceeds to the Company from the January 2025 Registered Direct Offering were $50.0 million. After deducting estimated placement agents’ fees and other offering expenses payable by the Company, net proceeds recorded as of December 31, 2025 were approximately $46.8 million.

In connection with the Registered Direct Offerings, the Company entered into placement agency agreements with A.G.P./Alliance Global Partners (“AGP”), pursuant to which AGP agreed to serve as the sole placement agent for the Company on a reasonable best efforts basis. In connection with the Registered Direct Offerings, the Company agreed to pay AGP an aggregate cash fee equal to 6.0% of the gross proceeds received in the respective offering. The securities in both Registered Direct Offerings were sold pursuant to the Company’s universal shelf registration statement on Form S-3, which was originally filed with the SEC on August 11, 2023, and related base prospectuses and prospectus supplements dated July 3, 2025 and January 3, 2025, respectively, thereunder.

Note 10. Stock-based Compensation

Equity Incentive Plan

The Quantum-Si Incorporated 2021 Equity Incentive Plan (the “2021 Plan”) provides for grants of stock options, stock appreciation rights, restricted stock, restricted stock units, and other stock or cash-based awards. Directors, officers and other employees of the Company and its subsidiaries, as well as others performing consulting or advisory services for the Company, are eligible for grants under the 2021 Plan. As of December 31, 2025, there were 14,602,612 shares available for future grant under the 2021 Plan.

Inducement Equity Incentive Plan

On May 8, 2023, the Company adopted the 2023 Inducement Equity Incentive Plan (the “2023 Inducement Plan”) to reserve 3,000,000 shares of its Class A common stock to be used exclusively for grants of awards to individuals that were not previously employees or directors of the Company as a material inducement to such individuals’ entry into employment with the Company within the meaning of Rule 5635(c)(4) of the Nasdaq Listing Rules. On August 23, 2024, the Company amended the 2023 Inducement Plan to reserve an additional 3,000,000 shares of its Class A common stock under the 2023 Inducement Plan. The terms and conditions of the 2023 Inducement Plan, as amended, are substantially similar to those of the 2021 Plan. As of December 31, 2025, there were 2,239,404 shares remaining available for issuance under the 2023 Inducement Plan.

Stock options

The Company granted an aggregate of 1,166,855 and 2,282,600 stock option awards to participants during the years ended December 31, 2025 and 2024, respectively, with vesting subject to the participant’s continued employment with or continued service provided to the Company through the applicable vesting dates.

During the year ended December 31, 2023, the Company granted an aggregate of 10,138,730 stock option awards to participants, with vesting subject to the participant’s continued employment with or continued service provided to the Company through the applicable vesting dates and, in specific instances, certain market conditions. These stock option awards included 2,000,000 stock options granted to the Chief Financial Officer which are subject to service and/or certain market conditions. The stock option awards granted to the Chief Financial Officer included 1,000,000 stock options issued from the 2021 Plan and 1,000,000 inducement stock options issued from the 2023 Inducement Plan which are subject to a service condition and certain market conditions. The service condition requires the Chief Financial Officer’s continued employment with the Company through the applicable vesting dates. The market conditions require the Company’s Class A common stock trade above a specified level for a defined period of time. The fair value of awards with market conditions was estimated at the grant date using the Monte Carlo simulation model.

Stock-based compensation related to stock options for the years ended December 31, 2025, 2024 and 2023 was $6.3 million, $6.4 million and $7.1 million, respectively. The Company estimates and records the compensation cost associated with the grants described above with an offsetting entry to paid-in capital. The Company utilized the Black-Scholes model for determining the estimated fair value for service or performance-based stock-based awards. The Black-Scholes model requires the use of subjective assumptions which determine the fair value of stock-based awards. The assumptions used to value option grants to employees and non-employees for the years ended December 31, 2025, 2024 and 2023 were as follows:

A summary of the stock option activity is presented in the table below:

The total fair value of stock options that vested during the years ended December 31, 2025 and 2024 was approximately $5.4 million and $6.4 million, respectively.

As of December 31, 2025 total unrecognized stock-based compensation related to stock options was $6.0 million, which is expected to be recognized over a remaining weighted average vesting period of 1.5 years.

Modification of Performance Stock Options

In November 2022 and May 2023, the Company granted 2,780,000 and 1,000,000 performance-based stock option awards to its Chief Executive Officer and Chief Financial Officer, respectively. The vesting of these awards are subject to continued service to the Company and certain market conditions. The market conditions require the Company’s Class A common stock trade above specified levels for certain periods of time. The fair values of the awards were estimated at the grant date using the Monte Carlo simulation model.

On March 15, 2024, the market conditions that trigger the vesting of these performance-based stock option awards were modified. The modified market conditions require the Company’s Class A common stock to trade above specified levels for certain defined periods of time that are different from the original awards. The Company accounted for the modifications as modifications of market conditions. The total incremental stock-based compensation expense to be recognized for these awards is approximately $2.4 million within Selling, general and administrative operating expenses in the Consolidated Statements of Operations and Comprehensive Loss. Incremental stock-based compensation expense was $0.8 million and $0.6 million for the years ended December 31, 2025 and 2024, respectively. There wereno such modifications to performance-based stock option awards for the year ended December 31, 2023.

Restricted stock units

During the years ended December 31, 2025, 2024 and 2023, the Company granted an aggregate of 8,535,732,9,216,559 and 786,938, respectively, of restricted stock unit (“RSU”) awards to participants with vesting subject to the participant’s continued employment with or continued service provided to the Company through the applicable vesting dates.

Stock-based compensation related to RSU awards for the years ended December 31, 2025, 2024 and 2023 was $4.5 million, $2.4 million and $1.4 million, respectively.

The number of shares and weighted average grant date fair values of restricted non-vested common stock at the beginning and end of 2025, as well as restricted stock units granted, vested, and forfeited during the year were as follows:

As of December 31, 2025 total unrecognized stock-based compensation related to restricted stock was $13.4 million, which is expected to be recognized over the remaining weighted average vesting period of 2.9 years.

The total fair value of restricted stock vested during the years ended December 31, 2025 and 2024 was approximately $4.2 million and $2.6 million, respectively.

Stock-based Compensation Expense

Stock-based compensation is allocated to Research and development and Selling, general and administrative operating expenses in the Consolidated Statements of Operations and Comprehensive Loss. Stock-based compensation expense for the years ended December 31, 2025, 2024 and 2023 is as follows (in thousands):

No related tax benefits of the stock-based compensation expense have been recognized and no related tax benefits have been realized from the exercise of stock options due to the Company’s net operating loss carryforwards.

Note 11. Warrant Liabilities

Public Warrants

As of December 31, 2025 and 2024, there was an aggregate of 3,833,317 and 3,833,319, respectively, ofoutstanding Public Warrants which entitle the holder to acquire Class A common stock. Each whole warrant entitles the registered holder to purchaseone share of Class A common stock at an exercise price of $11.50 per share, subject to adjustment as discussed below, beginning on September 9, 2021. The warrants will expire on June 10, 2026 or earlier upon redemption or liquidation.

Redemptions

At any time while the warrants are exercisable, the Company may redeem not less than all of the outstanding Public Warrants:

•in whole and not in part;

•at a price of$0.01 per warrant;

•upon not less than 30 days’ prior written notice of redemption (the “30-day redemption period”) to each warrant holder; and

•if, and only if, the closing price of the Company’s common stock equals or exceeds$18.00 per share (as adjusted for stock splits, stock capitalizations, reorganizations, recapitalizations and the like) for any 20 trading days within a 30-trading day period ending three business days before the Company sends the notice of redemption to the warrant holders.

If the foregoing conditions are satisfied and the Company issues a notice of redemption of the Public Warrants at $0.01 per warrant, each holder of Public Warrants will be entitled to exercise his, her or its Public Warrants prior to the scheduled redemption date.

If the Company calls the Public Warrants for redemption for $0.01 as described above, the Company’s Board of Directors may elect to require any holder that wishes to exercise his, her or its Public Warrants to do so on a “cashless basis.” If the Company’s Board of Directors makes such election, all holders of Public Warrants would pay the exercise price by surrendering their warrants for the number of shares of Class A common stock equal to the quotient obtained by dividing (x) the product of the number of shares of Class A common stock underlying the warrants, multiplied by the excess of the “fair market value” over the exercise price of the warrants by (y) the “fair market value.” For purposes of the redemption provisions of the warrants, the “fair market value” means the average last reported sale price of the Class A common stock for the 10 trading days ending on the third trading day prior to the date on which the notice of redemption is sent to the holders of warrants.

The Public Warrants do not meet the criteria to be classified in stockholders’ equity as the exercise of the warrants may be settled in cash upon the occurrence of a tender offer or exchange offer in which the maker of the tender offer or exchange offer, upon completion of the tender offer or exchange offer, beneficially owns more than 50% of the outstanding shares of the Company’s Class A common stock, even if it would not result in a change of control of the Company. This provision precludes the Public Warrants from being classified in equity and thus, they are classified as current and long-term liabilities on the Condensed Consolidated Balance Sheets as of December 31, 2025 and 2024, respectively.

Private Warrants

There were 135,000 Private Warrants outstanding as of December 31, 2025 and 2024. The Private Warrants are identical to the Public Warrants, except that so long as they are held by the Sponsor or any of its permitted transferees, (i) the Private Warrants and the shares of Class A common stock issuable upon the exercise of the Private Warrants were not transferable, assignable or saleable until 30 days after the completion of the Business Combination, (ii) the Private Warrants will be exercisable for cash or on a cashless basis, at the holder’s option, and (iii) the Private Warrants are not subject to the Company’s redemption option at the price of $0.01 per warrant. The Private Warrants are subject to the Company’s redemption option at the price of $0.01 per warrant, provided the other conditions of such redemption are met, as described above. If the Private Warrants are held by a holder other than the Sponsor or any of its permitted transferees, the Private Warrants will be redeemable by the Company in all redemption scenarios applicable to the Public Warrants and exercisable by such holders on the same basis as the Public Warrants.

The Private Warrants do not meet the criteria to be classified in stockholders’ equity as the terms of the warrants provide for potential changes to the settlement amounts depending upon the characteristics of the warrant holder, and because the holder of a warrant is not an input into the pricing of a fixed-for-fixed option on equity shares. This provision precludes the Private Warrants from being classified in equity and thus, they are classified as current and long-term liabilities on the Condensed Consolidated Balance Sheets as of December 31, 2025 and 2024, respectively.

The fair value of warrant liabilities was $0.8 million and $5.0 million as of December 31, 2025 and 2024, respectively. The Company recognized a gain of $4.2 million and losses of $3.7 million and $0.3 million for the years ended December 31, 2025, 2024 and 2023, respectively, as a Change in fair value of warrant liabilities in the Consolidated Statements of Operations and Comprehensive Loss. There weretwo exercises andno redemptions of the Public Warrants andno exercises or redemptions of the Private Warrants during the year ended December 31, 2025. There wereno exercises or redemptions of the Public Warrants or Private Warrants during the years ended December 31, 2024 and 2023.

For further details regarding the warrant liabilities, please refer to Note 4. Fair Value of Financial Instruments.

Note 12. Net Loss Per Share

The Company presents both basic earnings per share (“EPS”) and diluted EPS. Basic and diluted net loss per share was the same for each period presented as the inclusion of all common share equivalents would have been anti-dilutive.

The following table presents the calculations for the years ended December 31, 2025,2024 and 2023 of basic and diluted net loss per share for the Company’s common stock (in thousands, except per share amounts):

Net loss per share attributable to Class A and Class B common stockholders was the same on a basic and diluted basis, as the inclusion of all potential common equivalent shares outstanding would have been anti-dilutive.

The following potential dilutive shares were excluded from the calculation of diluted net loss per share because their effect would be anti-dilutive for the years ended December 31, 2025,2024 and 2023:

Note 13. Restructuring

The Company committed to organizational restructurings during the fourth quarter of 2024, designed to decrease its costs and create a more streamlined organization to support its business. These liabilities are included in Accrued expenses and other current liabilities on the Consolidated Balance Sheets.

The Company’s restructuring costs, primarily for cash severance and other severance costs, are allocated to the following operating expense categories as follows (in thousands):

(1) Restructuring charges incurred and Cash payments and other adjustments include non-cash charges related to stock-based compensation expense and charges for cash severance and other severance costs, including health care coverage for a specified period of time after separation.

The Company’s restructuring activities were complete as of December 31, 2024 and, as of December 31, 2025, the Company does not expect to incur additional charges associated with these activities.

Note 14. Income Taxes

The components of (loss) income before provision for income taxes for the years ended December 31, 2025,2024 and 2023 are as follows (in thousands):

The provision for income taxes for the years ended December 31, 2025,2024 and 2023 consists of the following (in thousands):

The table below provides the updated requirements of ASU 2023-09 for the year ended December 31, 2025. For further discussion related to ASU 2023-09, please refer to Note 2. Summary of Significant Accounting Policies. For purposes of reconciling the Company’s provision for income taxes at the statutory rate and the Company’s provision for income taxes at the effective rate, a notional 21% tax rate was applied as follows:

(1)For the year ended December 31, 2025, the states and district that contributed to the majority (greater than 50%) of the tax effect in this category include California, Connecticut, District of Columbia, Massachusetts and New York.

As previously disclosed, for the years ended December 31, 2024 and 2023, prior to the adoption of ASU 2023-09, the effective income tax rate differs from the statutory federal income tax rate as follows:

The difference between the statutory federal income tax rate and the Company’s effective tax rate in 2024 and 2023 is primarily attributable to the effect of losses sustained which required a valuation allowance.

The amounts of cash income taxes paid by the Company are as follows (in thousands):

The tax effects of temporary differences that give rise to significant portions of the Company’s deferred tax assets and liabilities as of December 31, 2025 and 2024 related to the following (in thousands):

A valuation allowance is recorded to reduce deferred tax assets to the amount that is more likely than not to be realized based on an assessment of positive and negative evidence, including estimates of future taxable income necessary to realize future deductible amounts. A significant piece of objective negative evidence evaluated was the cumulative loss incurred over the three-year period ended December 31, 2025. Such objective evidence limits the ability to consider other subjective evidence such as its projections for future growth. On the basis of this evaluation, as of December 31, 2025 and 2024, the Company recorded a valuation allowance of $178.1 million and $156.5 million, respectively. The valuation allowance increased by $21.6 million and $17.0 million, for the years ended December 31, 2025 and 2024, respectively, due to losses incurred that cannot be realized.

As of December 31, 2025, the Company has accumulated federal and state net operating loss (“NOL”) carryforwards of $513.1 million and $355.8 million, respectively. Of the $513.1 million of federal NOL carryforwards, $65.5 million was generated before January 1, 2018 and is subject to the 20-year carryover period (“pre-Tax Act losses”) and begin to expire in 2033. The remaining $447.6 million can be carried forward indefinitely but is subject to the 80% taxable income limitation. Of the $355.8 million of state NOL carryforwards, $24.5 million can be carried forward indefinitely with the remaining beginning to expire in 2031.

In addition, the Company has federal and Connecticut research and development credit carryforwards totaling $8.1 million and $5.3 million, respectively. The federal research and development credits begin to expire in 2033 unless previously utilized. The Connecticut research and development credits do not expire.

The Company also has federal and state capital loss carryforwards totaling $20.1 million and $14.6 million, respectively. The capital losses start expiring in 2027 unless previously utilized.

Pursuant to Sections 382 and 383 of the Internal Revenue Code (“IRC”), annual use of the Company’s NOL and credit carryforwards may be limited in the event a cumulative change of ownership of more than 50% occurs within athree-year period. Since the Company’s formation, the Company has raised capital through the issuance of capital stock, which on its own or combined with the purchasing stockholders’ subsequent disposition of those shares, may have resulted in such an ownership change, or could result in an ownership change.

Upon the occurrence of an ownership change under Section 382 as outlined above, utilization of the Company’s NOL and research and development credit carryforwards are subject to an annual limitation, which is determined by first multiplying the value of the Company’s stock at the time of the ownership change by the applicable long-term tax-exempt rate, which could be subject to additional adjustments, as required. Any limitation may result in expiration of a portion of the NOL or research and development credit carryforwards before utilization. The Company has completed an analysis through December 31, 2025 and no such ownership change has occurred, however, an ownership change may occur in the future.

The Company recognizes liabilities for uncertain tax positions based on a two-step process. The first step is to evaluate the tax position for recognition by determining if the weight of available evidence indicates that it is more likely than not that the tax position will be sustained on audit, including resolution of related appeals or litigation processes if any. The second step is to measure the tax benefit as the largest amount that is more than 50% likely of being realized upon settlement. While the Company believes it has appropriate support for the positions taken on its tax returns, the Company regularly assesses the potential outcome of examinations by tax authorities in determining the adequacy of its provision for income taxes.

The following table summarizes the activity related to the Company’s gross unrecognized tax benefits as of December 31, 2025,2024 and 2023 (in thousands):

As of December 31, 2025, the Company had gross unrecognized tax benefits of $2.9 million which would affect the effective tax rate if recognized subject to valuation allowance. The Company’s policy is to recognize the interest expense and/or penalties related to income tax matters as a component of income tax expense. As of both December 31, 2025, the Company had no accrued interest and penalties recorded on its Consolidated Balance Sheets.

The Company is subject to taxation in the United States, various states within the United States, and France. The Company was notified in November 2024 that the Internal Revenue Service (“IRS”) will be examining their December 31, 2022 Federal income tax return. The audit commenced during 2025 and remains open as of December 31, 2025. As a result of the audit, the IRS proposed certain adjustments with respect to the tax reporting of our former executives’ 2022 compensation amounts, and the reclassification of an amount originally reported a net operating loss to a capital loss. Due to our current and historical loss position, the proposed adjustments would have no material impact on our Federal income tax; therefore, the Company has agreed to make the adjustments as proposed by the IRS. The net operating loss has been reduced by $7.4 million of which $4.4 million has been reclassified from net operating loss to capital loss. The Company has not been notified that it is under audit by any state or foreign taxing authorities, however, due to the presence of NOL carryforwards, all of the income tax years remain open for examination in each of these jurisdictions.

Additionally, as a result of legislation in the state of Connecticut and the country of France, companies have the opportunity to exchange certain research and development tax credit carryforwards for a cash refund. The research and development expenses that qualify for this benefit are limited to those costs incurred within each jurisdiction. The Company has elected to participate in these exchange programs and, as a result, has recognized net benefits of $2.6 million for the year ended December 31, 2025, and $0.2 million for each of the years ended December 31, 2024 and 2023, which are included in Research and development in the Consolidated Statements of Operations and Comprehensive Loss. As of December 31, 2025 and 2024, the Company recorded $0.7 million of the research and development tax credit receivables in Prepaid expenses and other current assets on the Company’s Consolidated Balance Sheets. As of December 31, 2025, all refunds for years prior to 2024 have been received by the Company.

The Company analyzes undistributed earnings of its foreign disregarded entity and has accrued withholding taxes of $0.1 million for earnings that are not permanently reinvested. No additional deferred tax liability has been established, as the parent entity would not be required to include the distribution into income as the amount would be tax free under current law.

On July 4, 2025, H.R.1, commonly referred to as the One Big Beautiful Bill Act, was enacted in the U.S., which includes a broad range of tax reform provisions, including extending and modifying certain key Tax Cuts and Jobs Act provisions (both domestic and international), and provisions allowing accelerated tax deductions for qualified property and research expenditures. The legislation has multiple effective dates, with certain provisions effective in 2025 and others to be implemented through 2027. The legislation’s enactment did not materially impact our effective income tax rate or cash tax position for the year ended December 31, 2025.

Note 15. Segment Information

Quantum-Si is a life sciences company focused on proteomics research, with the mission of transforming single-molecule analysis and democratizing its use by providing researchers and clinicians access to the proteome, the set of proteins expressed within a cell. The Company’s platform includes its Platinum NGPS instrument, Platinum Analysis Software, and consumable kits for use with its Platinum line of instruments.

The Company’s Chief Operating Decision Maker (the “CODM”), its Chief Executive Officer, reviews financial information presented on a consolidated basis for purposes of assessing financial performance, making operating decisions and allocating resources. Accordingly, the Company has determined it operates as a single reportable segment. The CODM utilizes the Company’s long-range plan, which includes product development roadmaps and long-range financial models, as a key input to resource allocation. The CODM makes decisions on resource allocation, assesses the performance of the business, and monitors budget versus actual results on a consolidated basis using loss from operations as reported in the Consolidated Statements of Operations and Comprehensive Loss as the primary measure of segment profit or loss. Net loss and the change in cash and cash equivalents and marketable securities are also measures considered in monitoring budget versus actual results.

Significant expenses within loss from operations, as well as within net loss, include research and development, and selling, general and administrative expenses, which are each separately presented on the Company’s Consolidated Statements of Operations and Comprehensive Loss. Other segment items included in net loss on the Company’s Consolidated Statements of Operations and Comprehensive Loss are lease termination expense, net, legal settlement expense, net of insurance proceeds, dividend income, interest income, change in fair value of warrant liabilities, other expense or income, net, and provision for income taxes.

The Company’s revenue is derived from sales of products and services. Product revenue is primarily generated from the sales of instruments and consumables used in protein sequencing and analysis. Service revenue is primarily generated from service maintenance contracts including access to analysis software and advanced training for instrument use.

Total revenue generated from domestic and international salesfor the years ended December 31, 2025, 2024 and 2023 is as follows (in thousands):

Note 16. Related Party Transactions

The Company was a party to the Amended and Restated Technology Services Agreement (the “ARTSA”), most recently amended on November 11, 2020, by and among 4Catalyzer Corporation (“4C”), the Company and other participant companies controlled by Dr. Jonathan Rothberg, the Chairman of the Company’s Board of Directors. The Company entered into a First Addendum to the ARTSA on February 17, 2021 pursuant to which the Company agreed to terminate its participation under the ARTSA no later than immediately prior to the effective time of the Business Combination, resulting in the termination of the Company’s participation under the ARTSA on June 10, 2021. In connection with the termination of the Company’s participation under the ARTSA, the Company terminated its existing arm’s length lease agreement with

4C and negotiated a new arm’s length lease agreement. Under the ARTSA, the Company and the other participant companies had agreed to share certain non-core technologies, which means any technologies, information or equipment owned or otherwise controlled by the participant company that are not specifically related to the core business area of the participant and subject to certain restrictions on use. The ARTSA also provided for 4C to perform certain services for the Company and each other participant company such as monthly administrative, management and technical consulting services to the Company which were pre-funded approximately once per quarter.

The Company incurred expenses paid to 4C in the amounts of $0.1 million, $0.3 million and $0.6 million during the years ended December 31, 2025, 2024 and 2023, respectively. These expenses included immaterial amounts for month-to-month sublease arrangements for office and laboratory spaces from 4C and certain administrative expenses. These expenses are included in Selling, general and administrative expenses in the Condensed Consolidated Statements of Operations and Comprehensive Loss.

The ARTSA also provided for the participant companies to provide other services to each other. There wereno amounts payable to or from the Company related to such services as of December 31, 2025 and 2024.

Effective November 1, 2022, the Company entered into an Advisory Agreement with Dr. Rothberg (the “Advisory Agreement”), pursuant to which Dr. Rothberg previously served as Chairman of the Board, advises the Chief Executive Officer and the Board on strategic matters, and provides consulting, business development and similar services on matters relating to the Company’s current, future and potential scientific and strategic initiatives and such other consulting services reasonably requested from time to time. Pursuant to the Advisory Agreement, as compensation for the services provided, in March 2023, the Company granted Dr. Rothberg an option to purchase 250,000 shares of Class A common stock pursuant to the 2021 Plan. In connection with the Advisory Agreement, Dr. Rothberg’s title was changed from Executive Chairman to Chairman of the Board. Subsequently, in May 2024, Dr. Rothberg’s title was changed from Chairman of the Board to Director.

Note 17. Commitments and Contingencies

Commitments

Licenses related to certain intellectual property:

The Company licenses certain intellectual property, some of which may be utilized in its current or future product offerings. To preserve the right to use such intellectual property, the Company is required to make annual minimum fixed payments totaling approximately $0.2 million as well as royalties based on net sales if the royalties exceed annual minimum fixed payments. As of both December 31, 2025 and 2024, the Company had accrued royalties of approximately$0.1 million included in Accrued expenses and other current liabilities on the Consolidated Balance Sheets.

Other commitments:

The Company sponsors a 401(k) defined contribution plan covering all eligible U.S. employees. Contributions to the 401(k) plan are discretionary. The Company didnot make any matching contributions to the 401(k) plan for the years ended December 31, 2025 and 2024.

Contingencies

The Company is subject to claims in the ordinary course of business. Except as discussed below, the Company is not currently a party to any pending or threatened litigation, the outcome of which would be expected to have a material adverse effect on its financial condition, results of operations, or cash flows. The Company discloses contingent liabilities even if the liability is not probable or estimable, or both, if there is a reasonable possibility a material loss may have been incurred.

Delaware Stockholder Litigation

On May 16, 2024, a punitive class action lawsuit was filed in the Delaware Court of Chancery, styled Farzad v. HighCape Capital, et al. (the “Delaware Stockholder Litigation”). The Delaware Stockholder Litigation asserts breach of fiduciary duty claims against the former officers and directors of HighCape, including Kevin Rakin, Matt Zuga, David Colpman, Robert Taub and Antony Loebel, HighCape Capital Acquisition LLC and HighCape Capital L.P.; aiding and abetting breach of fiduciary duty claims against Foresite Capital Management, LLC and Dr. Rothberg; and unjust enrichment claims against all defendants related to the Business Combination. The Delaware Stockholder Litigation complaint alleges that the transactions contemplated by the Business Combination were a product of an unfair process which was allegedly impacted by conflicts of interest, resulting in mispricing of the Business Combination. Quantum-Si, as part of the Business Combination, had previously agreed to indemnify certain of the defendants related to actions such as the Delaware Stockholder Litigation to the extent allowable by law.

On July 22, 2025, the parties of the Delaware Stockholder Litigation, through a mediation process, reached a preliminary settlement. As a result, as of December 31, 2025, the Company recorded a gross Accrued legal settlement liability of $8.0 million and a $4.6 million Legal settlement insurance receivable in the Consolidated Balance Sheets and associated legal settlement fees of $3.4 million in Legal settlement, net of insurance proceeds, in the Consolidated Statements of Operations and Comprehensive Loss during the year ended December 31, 2025. Of the $8.0 million accrued liability, $7.6 million represents the preliminary legal settlement amount and $0.4 million is an estimate of legal and related expenses to finalize the legal settlement.

On December 23, 2025, a Stipulation and Agreement of Compromise, Settlement, and Release in relation to the Delaware Stockholder Litigation (the “Settlement Agreement”) was executed. This Settlement Agreement is subject to the completion of a number of court procedural processes, including final court approval, which is scheduled for March 27, 2026. The Company has deemed these remaining court procedural processes as probable of occurring.

Contract Manufacturer Matter

In April 2023, the Company informed the contract manufacturer that had manufactured the Platinum and another development product, Carbon™, that it intended to wind down the relationship and transition to a different contract manufacturer. In October 2023, the former contract manufacturer filed a complaint against the Company in the State of Texas alleging breach of contract and made claims for economic damage and attorney costs. In January 2024, the suit was withdrawn and refiled in the State of Minnesota alleging similar claims. The Company denied all liability and countersued alleging claims of negligence. In August 2025, the Company paid $1.8 million to the former contract manufacturer to settle and discharge all claims. This amount is included in Legal settlement expense, net of insurance proceeds, in the Consolidated Statements of Operations and Comprehensive Loss.

Winchester Mutual Release Agreement

In December 2021, the Company signed a 10-year lease with Winchester Office LLC (“Winchester”) as landlord (the “Lease Agreement”) for approximately 67,000 square feet of space in New Haven, Connecticut(the “Premises”). The lease commenced on January 8, 2022 with rent payments beginning on July 7, 2022 and an original lease expiration date of July 31, 2032. Under the lease, Winchester contractually agreed to reimburse the Company for up to$9.1 millionin improvements to the space, to be used for such improvements as the Company deems “necessary or desirable”. On September 13, 2022, the Company filed a lawsuit against Winchester, alleging that Winchester had: (i) refused to reimburse the Company for costs related to improvements already incurred and submitted, (ii) delayed the Company’s completion of improvements, in order to avoid reimbursing the costs of those improvements, and (iii) improperly rejected the Company’s proposed improvement plans. On September 23, 2025, the Company and Winchester entered into the Mutual Release Agreement in connection with the Lease Agreement. Pursuant to the Mutual Release Agreement, the Company and Winchester agreed to terminate the Lease Agreement, effective as of September 23, 2025 (the “Early Termination Date”), subject to the terms and conditions therein. The Mutual Release Agreement provided that the Company surrender the Premises on or prior to the Early Termination Date. The Company had no further rent obligations after the Early Termination Date.

For the year ended December 31, 2025, the Company recorded $13.6 million of total Lease termination expense, net, in the Consolidated Statements of Operations and Comprehensive Loss related to the Mutual Release Agreement. Included in this amount is (i) consideration for Winchester’s agreement to terminate the Lease Agreement as of the Early Termination Date and settle all disputes between the parties in the gross amount of $11.0 million, less the surrender of a $0.6 million security deposit and a $0.2 million credit for the monthly recurring charges incurred for September 2025, resulting in a net cash payment of $10.2 million, (ii) the write-off of tenant improvement construction costs, which were not placed in service and which were included in construction in process within Property and equipment, net, on the Consolidated Balance Sheets, resulting in a loss of $1.2 million, (iii) the derecognition of $1.7 million of net operating lease right-of-use assets and related lease liabilities, and, (iv) the write-off related to the surrender of the $0.6 million security deposit.

Indemnification Provisions

The Company enters into agreements that contain indemnification provisions with other parties in the ordinary course of business, including business partners, investors, contractors, and the Company’s officers, directors and certain employees. The Company has agreed to indemnify and defend the indemnified party claims and related losses suffered or incurred by the indemnified party from actual or threatened third-party claims because of the Company’s activities or non-compliance with certain representations and warranties made by the Company. It is not possible to determine the maximum potential loss under these indemnification provisions due to the Company’s limited history of prior indemnification claims and the unique facts and circumstances involved in any particular case. To date, losses recorded in the Consolidated Statements of Operations and Comprehensive Loss in connection with the indemnification provisions have not been material.