Quanterix Corp

(unaudited)

Note 1. Organization and Nature of Business

Quanterix Corporation (“Quanterix” or the “Company”) is a life sciences company that has developed next-generation, ultra-sensitive digital immunoassay platforms that advance life sciences research and diagnostics. The Company’s platforms are based on its proprietary digital “Simoa” detection technology and enable customers to reliably detect protein biomarkers in ultra-low concentrations in blood, serum, and other fluids that, in many cases, are undetectable using conventional, analog immunoassay technologies. The ability of the Company’s Simoa platforms to detect proteins in the femtomolar range is enabling the development of novel therapies and diagnostics and has the potential to facilitate a paradigm shift in healthcare from an emphasis on treatment to a focus on earlier detection, monitoring, prognosis, and, ultimately, prevention.

The Company also provides contract research services for customers and Laboratory Developed Test (“LDT”) services through its Clinical Laboratory Improvement Amendments of 1988 (“CLIA”) certified Accelerator Laboratory (the “Accelerator Laboratory”). The Accelerator Laboratory provides customers with access to Simoa technology and its Lucent Diagnostics clinical testing services and supports multiple projects and services, including sample testing, homebrew assay development, custom assay development, and blood-based biomarker testing.

Note 2. Significant Accounting Policies

Basis of Presentation

The accompanying Consolidated Financial Statements and Notes to Consolidated Financial Statements have been prepared in accordance with generally accepted accounting principles in the United States of America (“U.S. GAAP”) and pursuant to the rules and regulations of the SEC regarding interim financial reporting on Form 10-Q. Accordingly, certain information and disclosures required for complete financial statements prepared in accordance with U.S. GAAP are not included. The Consolidated Balance Sheet and related information as of December 31, 2024 included herein was derived from the audited Consolidated Financial Statements as of December 31, 2024, but does not include all disclosures required by U.S. GAAP on an annual reporting basis. Certain amounts in the prior years’ Consolidated Financial Statements have been reclassified to conform to the current year’s presentation.

These Consolidated Financial Statements should be read in conjunction with the Company’s Annual Report on Form 10-K for the year ended December 31, 2024, as filed with the SEC on March 17, 2025. Since the date of that filing, there have been no changes or updates to the Company’s significant accounting policies, other than those described below.

In the opinion of management, the Consolidated Financial Statements and Notes to Consolidated Financial Statements contain all normal, recurring adjustments necessary for a fair statement of financial position, results of operations, comprehensive loss, and cash flows as of the dates and for the interim periods presented. The results of operations for the three and six months ended June 30, 2025 may not be indicative of the results for the full year ending December 31, 2025, or any other period.

The Company’s fiscal year is the 12-month period from January 1 through December 31, and all references to “2025,” “2024,” and the like refer to that fiscal year unless otherwise noted.

Use of Estimates

The preparation of the Consolidated Financial Statements and Notes to Consolidated Financial Statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities at the end of each fiscal period, and the reported amounts of revenues and expenses during each fiscal period. Such estimates include, but are not limited to, revenue recognition, valuation of inventory,valuation and impairment of goodwill, intangible and other long-lived assets, valuation of acquired assets and liabilities from acquisitions, valuation of contingent consideration, recoverability of deferred tax assets, and stock-based compensation expense. The Company bases its estimates on historical experience, known trends, worldwide economic conditions, both general and specific to the life sciences industry, and other relevant factors it believes to be reasonable under the circumstances. On an ongoing basis, management evaluates its estimates and changes in estimates are recorded in the period in which they become known. Actual results could differ from those estimates.

Principles of Consolidation

The Consolidated Financial Statements and Notes to Consolidated Financial Statements include the accounts of Quanterix and its wholly-owned subsidiaries. All intercompany transactions have been eliminated in consolidation.

In accordance with Accounting Standards Codification (“ASC”) 810 – Consolidation, the Company assesses the terms of non-marketable equity investments to determine if any meet the definition of a variable interest entity (“VIE”) and require consolidation into its Consolidated Financial Statements. Refer to Note 17 - Variable Interest Entities for further discussion.

Business Acquisition

On January 8, 2025, the Company acquired all of the issued and outstanding shares of capital stock of Emission, Inc., a privately held company based in Georgetown, Texas. Refer to Note 3 - Acquisitions for further discussion.

Foreign Currency

The functional currency of the Company’s subsidiaries are their respective local currencies. These subsidiary financial statements are translated into U.S. dollars using the period-end exchange rates for assets and liabilities, average exchange rates during the corresponding period for revenue and expenses, and historical rates for equity. The effects of foreign currency translation adjustments are recorded in accumulated other comprehensive loss, a component of stockholders’ equity on the Consolidated Balance Sheets.

Foreign currency transaction gains (losses) are included in other income (expense), net, on the Consolidated Statements of Operations and werenot material for the three months ended June 30, 2025 and 2024. Foreign currency losses were $0.3 million for the six months ended June 30, 2025 and foreign currency gains were $0.3 million for the six months ended June 30, 2024.

Restricted Cash

The following table summarizes the period ending cash and cash equivalents as presented on the Consolidated Balance Sheets and the total cash, cash equivalents, and restricted cash as presented on the Consolidated Statements of Cash Flows (in thousands):

(1) Restricted cash consists of collateral for a letter of credit issued as security for two of the Company’s leased facilities and to secure the Company’s corporate credit card program. The short-term or long-term classification is determined in accordance with the expiration of the underlying letter of credit and security.

Impairment of Goodwill

The Company assesses goodwill for impairment at the reporting unit level at least annually or whenever events or circumstances change that would more likely than not reduce the fair value of a reporting unit below its carrying amount. An impairment assessment requires evaluating a potential impairment using either a qualitative assessment, to determine if it is more likely than not that the fair value of any reporting unit is less than its carrying amount, or a quantitative analysis, to determine and compare the fair value of each reporting unit to its carrying value, or a combination of both. Judgment is required in determining the use of a qualitative or quantitative assessment, as well as in determining a reporting unit’s estimated fair value, as it requires us to make estimates of market conditions and operational performance, including items such as projected financial results, discount rates, control premium, or valuation multiples for key financial metrics.

During the three months ended June 30, 2025, the Company recorded an impairment charge on its entire goodwill balance. Refer to Note 4 - Goodwill and Intangible Assets for further discussion.

Impairment of Long-Lived Assets

The Company reviews its long-lived assets for impairment whenever events or circumstances indicate the carrying amount of the asset(s) may not be fully recoverable or that the estimated useful lives may warrant revision. To assess the recoverability of a long-lived asset or asset group, the Company compares the estimated undiscounted future cash flows for the estimated remaining useful life, or estimated lease term, of the asset (or the primary asset in the asset group) to its carrying value. If the undiscounted cash flows are less than the carrying value, the Company estimates the asset's fair value using the future discounted cash flows associated with the use of the asset. To the extent that the discounted cash flows are less than the carrying value, the asset(s) are impaired and written down to their estimated fair value.

Significant judgment is required to estimate future cash flows, including, but not limited to, estimates about future revenues, expenses, asset disposal value, expected uses of the asset (group), historical customer retention rates, technology roadmaps, customer awareness, trademark and trade name history, contractual provisions that could limit or extend an asset's useful life, market data, discount rates, and potential sublease opportunities including rent and rent escalation rates, time to sublease, and free rent periods.

The Company records costs associated with approved restructuring plans to reorganize operations. Restructuring costs are comprised of employee separation costs, primarily severance and related benefit payments, and any associated costs related to implementing a restructuring plan.

The Company records restructuring charges when a restructuring plan is approved and the amounts to be incurred are estimable. Refer to Note 19 - Restructuring Costs for further discussion on the restructuring plan implemented during the three months ended June 30, 2025.

Recent Accounting Standards to be Adopted

In December 2024, the FASB issued Accounting Standards Update (“ASU”) No. 2023-09, Income Taxes (Topic 740): Improvements to Income Tax Disclosures. The new standard enhances annual income tax disclosure requirements by requiring specified categories and greater disaggregation within the tax rate reconciliation table, disclosure of income taxes paid by jurisdiction, and additional disclosures of uncertain tax positions and the related financial statement impacts. The new standard will be effective for the Company for annual reporting periods beginning after December 15, 2024, with early adoption permitted. The Company expects that adoption of the standard will increase its income tax related disclosures but will not have a material impact on its Consolidated Financial Statements.

In November 2024, the FASB issued ASU No. 2024-03, Reporting Comprehensive Income (Topic 220): Expense Disaggregation Disclosures. This update enhances disclosure of an entity's expenses, primarily through additional disaggregation of income statement expenses. The update also requires entities to disclose qualitative descriptions of the amounts remaining in relevant expense captions that are not separately disaggregated quantitatively. The amendments in this update can be applied prospectively or retrospectively. The new standard will be effective for the Company for annual reporting periods beginning after December 15, 2026 and interim reporting periods beginning after December 15, 2027. The Company is currently evaluating the impact of adoption of the standard on its Consolidated Financial Statements disclosures.

Note 3. Acquisitions

The Company accounts for business combinations in accordance with the acquisition method of accounting under ASC 805 -Business Combinations (“ASC 805”). The acquisition method of accounting requires the Company to record the acquired assets and liabilities, including identifiable intangible assets, at their estimated fair values as of the acquisition date, with any excess of the consideration transferred recorded to goodwill.

On January 8, 2025, the Company acquired all of the issued and outstanding shares of capital stock of Emission, Inc. (“Emission”), a life sciences manufacturing company based in Georgetown, Texas. Emission produces large-scale, highly-uniform dye-encapsulating magnetic beads designed for low and mid-plex assays and a mid-plex platform that reads these proprietary beads. The transaction is part of the Company's plans to secure the use of Emission’s highly controlled beads in the Company's next generation platforms and expansion into a new multi-plex market segment targeting third-party original equipment manufacturer customers.

Total Consideration Transferred

The following table summarizes the fair value of the aggregate consideration paid or payable for Emission as of the acquisition date (in thousands):

(1)Cash paid at close represents the contractual amount paid on the closing date and is reflected as an investing activity in the Consolidated Statements of Cash Flows. Cash acquired was not material.

(2)The holdback is expected to be paid during the first quarter of 2026 and is subject to applicable adjustments.

(3)The acquisition includes contingent consideration discussed below in the section titled “Contingent Payments”.

Contingent Payments

The Emission transaction includedtwo arrangements that could result in additional cash payments to the seller. An additional $10.0 million is payable upon completion of certain technical milestones (“Earnout 1”) and up to $50.0 million could be payable based on the amount and timing of certain performance targets over afive year period ending December 31, 2029 (“Earnout 2”).

Under ASC 805, the Company determined Earnout 1 is compensation expense and is therefore recognized separately from the business combination. In accordance with ASC 710 -Compensation, Earnout 1 is recognized over the expected period certain technical requirements are transferred and certain milestones are completed, which the Company currently estimates to beeight months from the closing date of the acquisition. This expense is recorded in research and development and selling, general and administrative expenses on the Consolidated Statements of Operations.

The preliminary fair value of Earnout 2 on the acquisition date was $6.6 million, which represents purchase price and is included in the accounting for the business combination. Monte-Carlo simulations were used to determine the fair value, including the following significant unobservable inputs: projected revenue, a risk adjusted discount rate, and revenue volatility. Refer to Note 8 - Fair Value of Financial Instruments for discussion on the fair value considerations for Earnout 2.

Preliminary Allocation of Purchase Price

The following table summarizes the preliminary allocation of the purchase price to the estimated fair values of the acquired assets and liabilities as of the acquisition date (in thousands):

(1)The acquired intangible asset is finite-lived, represents developed technology, and has an estimated useful life of 14 years. The determination of the fair value of the finite-lived intangible asset required management judgment and the consideration of a number of factors. In determining the fair value, management primarily relied on a multi-period excess earnings valuation methodology. This methodology required the use of estimates, including projected revenues related to the particular asset; its obsolescence rate; royalty, margin, and discount rates; and certain published or readily available industry benchmark data. In establishing the estimated useful life of the acquired intangible asset, the Company relied primarily on the duration of the cash flows utilized in the valuation model.

(2)Goodwill represents the expected synergies from combining Emission with Quanterix as well as the value of the acquired workforce. The goodwill is not deductible for income tax purposes. As of June 30, 2025, the Company has booked a full impairment of the goodwill (refer to Note 4 - Goodwill and Intangible Assets).

(3)Recorded in other non-current liabilities on the Consolidated Balance Sheets.

The purchase price allocation set forth above is preliminary as the Company continues to obtain information to complete the purchase price allocation. The Company will record adjustments, if any, during the measurement period subsequent to the acquisition date and bases such adjustments only on facts and circumstances that existed as of the acquisition date. Measurement period adjustments since the acquisition date have not been material.

The operating results of Emission have been included in the Company's financial statements since the acquisition date and are not material to the Company's consolidated financial results.

Acquisition costs related to the Emission transaction were not material for the three and six months ended June 30, 2025.

Call Option Agreement

In connection with the closing of the acquisition of Emission, the Company entered into a call option agreement (the “Option Agreement”), in which the Emission selling shareholders have the right to repurchase all of the outstanding capital stock of Emission for $10.0 million after five years if Emission’s revenues do not exceed $5.0 million in any one year during such five-year period. If the Emission selling shareholders exercise the right to repurchase Emission, the Company will retain a perpetual, fully-paid, irrevocable license to all Emission intellectual property required to continue to manufacture and commercialize the Company's products. The Company determined that the call option is embedded in the purchased shares of Emission and does not require separate accounting unless exercised.

Note 4. Goodwill and Intangible Assets

Goodwill and Impairment

Goodwill represents the amount an acquisition’s purchase price exceeds the fair value of the assets acquired, including identifiable intangible assets, and liabilities assumed. Goodwill is not amortized; however it is required to be tested for impairment annually at the reporting unit level. Testing for impairment is also required on an interim basis if events or circumstances indicate it is more likely than not that an impairment loss has been incurred.

A reporting unit is defined as an operating segment or a component of an operating segment to the extent discrete financial information is available that is reviewed by segment management. The Company has determined it hasone reporting unit.

Absent an event that indicates a specific impairment may exist, the Company has selected October 1 as the date for performing its annual goodwill impairment test. The impairment test is first performed at the reporting unit level using a qualitative assessment to determine whether it is more likely than not that the fair value of the reporting unit is less than its carrying value. If the reporting unit does not pass the qualitative assessment, then the reporting unit’s carrying value is compared to its fair value. Goodwill is considered impaired if the carrying value of the reporting unit exceeds its fair value, and an impairment loss is recognized in amount equal to this excess.

During the second quarter of 2025, the Company assessed several events and circumstances, including a larger than expected decline in the Company's revenue and bookings primarily due to the rapidly changing macro-economic conditions resulting from reductions in US federal research funding, reductions in research and development spending by larger pharmaceutical customers, and new import tariffs. As a result, the Company concluded it was more likely than not that that the fair value of its single reporting unit was less than its carrying value and performed a quantitative impairment test for its goodwill as of June 30, 2025.

The Company estimated the implied fair value of its reporting unit using a market valuation approach, which included inputs such as the Company's quoted stock price.

As a result of the quantitative test, the Company determined its goodwill was fully impaired and recorded an impairment charge of $6.4 million during the three months ended June 30, 2025. The Company did not record a goodwill impairment in any other periods presented.

Changes in the carrying amount of goodwill are as follows (in thousands):

Intangible Assets, Long-Lived Assets, and Impairment

The Company continually assesses the determination of its asset groups, which primarily focuses on changes in the Company's operating structure, the way in which it expects to deploy its assets, or how the Company intends to recover the cost of it assets. As a result of the acquisition of Emission, the Company reassessed its asset groups. Primarily due to management's updated expectations of how it plans to deploy and recover the costs of its assets, the Company determined the assets acquired in the Emission acquisition would become their own asset group.

Prior to the quantitative goodwill impairment test, the Company tested the recoverability of its long-lived assets, including intangible assets and property and equipment. The Company utilized an undiscounted cash flow analysis to determine if the cash flows expected to be generated by its asset groups over the remaining estimated useful lives of each group's primary asset were sufficient to recover the carrying value of each asset group. Significant assumptions that form the basis of the forecasted results utilized to calculate undiscounted cash flows include estimates about future revenues, expenses, and market conditions related to these assets, as well as the disposal value of the asset group. These estimates are based on a complex series of judgments about future events and rely heavily on estimates and assumptions that have been deemed reasonable by the Company. Changes in the estimates or assumptions used could materially affect the determination of recoverability. Potential events and circumstances that could have an adverse impact on our estimates and assumptions include, but are not limited to, lower than expected bookings growth, increases in costs, and other macroeconomic factors. As of June 30, 2025, the Company concluded that none of its intangible or other long-lived assets were impaired.

Should economic conditions deteriorate further or remain depressed for a prolonged period of time, estimates of future cash flows for each of the Company’s asset groups may be insufficient to support their carrying value, requiring an impairment. Impairment charges, if any, may be material to the results of operations and financial position.

Acquired intangible assets consisted of the following (in thousands, except useful life and weighted average life amounts):

The Company recorded amortization expense of $0.6 million and $0.4 million for the three months ended June 30, 2025 and 2024, respectively, and $1.2 million and $0.8 million for the six months ended June 30, 2025 and 2024, respectively.

Future estimated amortization expense is as follows (amounts in thousands):

Note 5. Revenue and Related Matters

Revenue from Contracts with Customers

The Company’s customers primarily consist of entities engaged in life sciences research that pursue the development of novel therapies and diagnostics for a variety of neurologic, oncologic, cardiovascular, and infectious diseases, and through the identification and measurement of protein biomarkers associated with diseases. The Company’s customer base includes pharmaceutical, biotechnology, contract research organizations, academic, and government institutions.

Disaggregated Revenue

The following table disaggregates the Company’s revenue from contracts with customers by geography, based on the location products and services are consumed, and revenue type (in thousands):

For the three and six months ended June 30, 2025 and 2024, no customer accounted for more than 10% of the Company’s total revenues. As of June 30, 2025 and December 31, 2024, no customer accounted for more than 10% of the Company’s gross accounts receivable.

Contract Assets

There wereno contract assets as of June 30, 2025 or December 31, 2024.

Deferred Revenue

During the three months ended June 30, 2025 and 2024, the Company recognized $3.1 million and $2.2 million of revenue, respectively, related to its deferred revenue balance at January 1 of each such period. During the six months ended

June 30, 2025 and 2024, the Company recognized $5.6 million and $4.9 million of revenue, respectively, related to its deferred revenue balance at January 1 of each such period.

Remaining Performance Obligations

As of June 30, 2025, the aggregate amount of transaction prices allocated to performance obligations that were not yet satisfied, or were partially satisfied, was $10.5 million. Of this amount, $9.4 million is expected to be recognized as revenue in the next 12 months, with the remainder expected to be recognized thereafter. The $10.5 million primarily consists of amounts billed for undelivered services related to initial and extended service-type warranties and research services.

Costs to Obtain a Contract

Changes in costs to obtain a contract were as follows (in thousands):

The Company evaluates potential impairment of these amounts at each balance sheet date andno impairments were recorded during the three and six months ended June 30, 2025 and 2024.

Grant Revenue

All of the Company's grant revenue is generated within North America.

NIH Grant

On September 21, 2022, the Company and the National Institutes of Health (the “NIH”), an agency of the U.S. Department of Health and Human Services, entered into a contract (the “NIH Grant”) with a total award value of $1.7 million. The NIH granted the Company funding in support of the development of certain point-of-care diagnostic technologies through collaborative efforts. Grant funding is to be used solely for activities related to the point-of-care diagnostic device development project and the contract period runs through August 2025. Receipt of the award value occurs throughout the term of the contract period and after the Company submits for reimbursement of activities related to the grant. As of June 30, 2025, the Company had received $1.5 million of the total award value.

During each of the three and six months ended June 30, 2025, NIH grant revenue recognized and research and development expenses incurred werenot material. During the three and six months ended June 30, 2024, NIH grant revenue recognized and research and development expenses incurred werenot material and $0.4 million, respectively.

Note 6. Allowance for Credit Losses

The change in the allowance for expected credit losses on accounts receivable is summarized as follows (in thousands):

Note 7. Marketable Securities

All of the Company's marketable securities are classified as available-for-sale. The amortized cost, gross unrealized gains, gross unrealized losses, and fair value of the Company’s marketable securities, by major security type, were as follows (in thousands):

The following tables show the fair value and gross unrealized losses of the Company’s marketable securities aggregated by major security type and length of time that the individual securities have been in a continuous unrealized loss position (in thousands):

The Company did not have any individual securities in a continuous loss position for greater than 12 months, and there were no individual securities that were in a significant unrealized loss position as of June 30, 2025. For marketable securities in an unrealized loss position, the Company does not intend to sell them, it is not more likely than not that the Company will be required to sell them before recovery of their amortized cost bases, and the unrealized losses are not credit related. Accordingly, the Company has not recorded any impairment losses or a credit loss allowance.

During the six months ended June 30, 2025, the Company sold $12.7 million of marketable securities. Realized gains related to the sale were not material.

At June 30, 2025 and December 31, 2024, the Company had $1.2 million and $1.5 million, respectively, of accrued interest receivable on its marketable securities.

The following table summarizes the contractual maturities of the Company’s marketable securities (in thousands):

Note 8. Fair Value of Financial Instruments

Recurring Fair Value Measurements

The following tables present the Company’s fair value hierarchy for its financial assets and liabilities that are measured at fair value on a recurring basis (in thousands):

(1)Included in cash and cash equivalents on the Consolidated Balance Sheets.

(2)Earnout 2 included in the acquisition of Emission (refer to Note 3 - Acquisitions) requires additional consideration to be paid to the selling shareholders based on the amount and timing of certain performance targets over afive year period ending December 31, 2029.

Cash equivalents and marketable securities classified as Level 2 financial assets are initially valued at their purchase price and subsequently valued at the end of each reporting period utilizing third party pricing services or other observable data. The pricing services utilize industry standard valuation methods, including both income and market-based approaches, and observable market inputs to determine the fair value. These observable market inputs include reportable trades, benchmark yields, credit spreads, broker/dealer quotes, bids, offers, current spot rates, and other industry and economic events.

The following table presents the changes in the Company's Level 3 financial instruments measured at fair value on a recurring basis:

(1)Refer to Note 3 - Acquisitions.

(2)Changes in fair value subsequent to the acquisition date were due to updated valuation inputs and the passage of time. Monte-Carlo simulations were used to determine the fair value, including the following significant unobservable inputs: projected revenue, a risk adjusted discount rate, and revenue volatility. Increases or decreases in the inputs would have resulted in a higher or lower fair value measurement. The range of outcomes payable iszero to $50.0 million. The fair value of the contingent consideration is recorded in accrued expenses and other current liabilities and non-current portion of contingent consideration on the Consolidated Balance Sheets. The change is recorded in change in fair value of contingent consideration on the Consolidated Statements of Operations.

Nonrecurring Fair Value Measurements

The Company has a non-marketable equity investment in a privately held entity. Since there is minimal market activity or other financial information available to determine the fair value of the shares held by Quanterix, this investment is considered a Level 3 financial asset.

Pursuant to ASC 321 –Investments – Equity Securities, the Company uses the measurement alternative for equity investments without readily determinable fair values and recognizes its equity investment at cost, less any impairment, adjusted for any observable price changes in orderly transactions. The shares received were valued at $0.8 million upon receipt, primarily using the third-party purchase price of similar interests. Changes in the inputs and assumptions used would have resulted in a higher or lower fair value measurement.

The Company’s non-marketable equity investment contains certain restrictions related to the sale or transfer of the securities. The restrictions are in place indefinitely and cannot lapse.

During the three and six months ended June 30, 2025, the Company did not record any fair value adjustments to its non-marketable equity investment. To date, the cumulative fair value adjustments have not been material. As of June 30, 2025 and December 31, 2024, the carrying value of the non-marketable equity investment was $0.8 million, and is recorded in other non-current assets on the Consolidated Balance Sheets. Refer to Note 17 - Variable Interest Entities for the Company's evaluation of investments in other entities under the VIE guidance.

Other Fair Value Disclosures

During the three months ended June 30, 2025 and 2024, the Company did not transfer financial assets between levels of the fair value hierarchy. Additionally, there have been no changes to the valuation techniques for Level 2 or Level 3 financial assets or liabilities.

Note 9. Inventory

Inventory, net of inventory reserves, consisted of the following (in thousands):

Note 10. Accrued Expenses and Other Current Liabilities

Accrued expenses and other current liabilities consisted of the following (in thousands):

(1)Represents the current portion of contingent compensation from Earnout 1 related to the Emission acquisition. Refer to Note 3 - Acquisitions.

Note 11. Stockholders' Equity

The following tables summarize the changes in equity during the three months ended June 30, 2025 and 2024, respectively (amounts in thousands):

Note 12. Stock-Based Compensation

Stock Options

Stock option activity for the six months ended June 30, 2025 is presented below (in thousands, except per share and contractual life amounts):

Restricted Stock Units

Restricted stock unit (“RSU”) activity for the six months ended June 30, 2025 is presented below (in thousands, except per share amounts):

Employee Stock Purchase Plan (“ESPP”)

During the six months ended June 30, 2025, employees purchased 102 thousand shares of the Company’s common stock pursuant to the 2017 Employee Stock Purchase Plan.

Stock-Based Compensation Expense

Stock-based compensation expense was recorded in the following categories on the Consolidated Statements of Operations (in thousands):

As of June 30, 2025, total unrecognized stock-based compensation expense related to unvested RSUs and stock options was $48.4 million, which is expected to be recognized over the remaining weighted-average vesting period of 2.7 years.

Note 13. Net Loss Per Share

The following table presents the computation of basic and diluted net loss per share (in thousands, except per share data):

As the Company was in a net loss position for all periods listed in the table below, the following common share equivalents (calculated on a weighted average basis) were excluded from the calculation of diluted net loss per share (in thousands):

Note 14. Income Taxes

The Company’s effective tax rates were 0.2% and 5.6% for the three and six months ended June 30, 2025, respectively, and (1.6)% for both the three and six months ended June 30, 2024, respectively. The effective tax rate in 2025 is higher than 2024 due to a non-recurring benefit of $3.0 million relating to the release of a portion of the Company's valuation allowance due to taxable temporary differences recorded as part of the Emission acquisition, which are a source of income to realize certain pre-existing federal and state deferred tax assets. The income tax provision and effective tax rate is driven primarily by a valuation allowance in the United States, partially offset by income taxes in foreign jurisdictions.

The Company maintains a valuation allowance on the majority of its deferred tax assets, and it has concluded that it is more likely than not that the deferred assets will not be utilized.

On July 4, 2025, the One Big Beautiful Bill Act (“OBBBA”) was enacted in the U.S. The OBBBA includes significant provisions impacting taxes, such as the permanent extension of certain expiring provisions of the Tax Cuts and Jobs Act, modifications to the international tax framework and the restoration of favorable tax treatment for certain business provisions. The legislation has multiple effective dates, with certain provisions effective in 2025 and others implemented through 2027. The Company is currently assessing the impact of the OBBBA on its Consolidated Financial Statements.

Note 15. Commitments and Contingencies

Purchase Commitments

STRATEC

During the second quarter of 2025, the Company and STRATEC Consumables GmbH (“STRATEC”) entered into the third amendment to the supply agreement with STRATEC (the “Amended STRATEC Supply Agreement”), effective as of January 1, 2025, related to the manufacturing of certain Simoa instruments. As part of the Amended STRATEC Supply

Agreement, the Company agreed to purchase a minimum number of instruments in 2025 and 2026 at agreed upon pricing. The Company may also be required to pay an additional annual maintenance fee based on the number of instruments purchased during 2025 and 2026, respectively. The agreement may be terminated upon 12 months notice after the later of meeting the minimum purchases or December 31, 2026.

The total purchase commitment for instruments under the Amended STRATEC Supply Agreement is approximately $10.8 million. There were no purchases made under the Amended STRATEC Supply Agreement during the three and six months ended June 30, 2025.

Other Purchase Commitments

The Company’s other non-cancellable purchase commitments primarily consist of purchases of raw materials for manufacturing operations under annual and multi-year agreements, some of which have minimum quantity requirements. As of June 30, 2025, the Company’s total purchase commitments under these agreements were $0.9 million.

License Agreements

Eli Lilly and Company

In February 2022, the Company and Eli Lilly and Company (“Lilly”) entered into a Technology License Agreement (the “Lilly License”) under which Lilly granted a non-exclusive license to Lilly’s proprietary p-Tau 217 antibody technology for use by the Company in research use only products, services, and future in vitro diagnostics (“IVD”) applications within the field of Alzheimer’s disease. Pursuant to the Lilly License, the Company paid an upfront fee, is required to make milestone payments based on the achievement of predetermined regulatory and commercial events, and will pay royalties on net sales of licensed products.

Harvard University

In August 2022, the Company and Harvard University (“Harvard”) entered into an exclusive license agreement (the “Harvard License Agreement”) for certain intellectual property owned by Harvard. Pursuant to the Harvard License Agreement, the Company paid an upfront fee of $0.6 million and is required to pay Harvard low single-digit royalties on net sales of products and services using the licensed technology, as well as a portion of its applicable sublicense revenues. The Company incurredno royalty expense under the Harvard License Agreement for the three and six months ended June 30, 2025 and 2024.

Refer to Note 16 - Related Party Transactions for a discussion of a related party relationship with Harvard.

Tufts University

In June 2007, the Company and Tufts University (“Tufts”) entered into a license agreement (the “Tufts License Agreement”) for certain intellectual property owned by Tufts. The Tufts License Agreement, which was subsequently amended, is exclusive and sub-licensable, and will continue in effect on a country-by-country basis as long as there is a valid claim of a licensed patent in a country. The Company is required to pay license and maintenance fees that are creditable against royalties, in addition to low single-digit royalties on direct sales and services, and a royalty on sublicense income. The Company incurred royalty expenses related to the Tufts License Agreement of $0.4 million and $0.8 million during the three and six months ended June 30, 2025, respectively, and $0.6 million and $1.1 million during the three and six months ended June 30, 2024, respectively, which were recorded in cost of product revenue on the Consolidated Statements of Operations.

Refer to Note 16 - Related Party Transactions for a discussion of a related party relationship with Tufts.

Legal Contingencies

The Company is subject to claims in the ordinary course of business; however, 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 or results of operations.

Leases

The undiscounted future lease payments for non-cancelable operating leases were as follows (in thousands):

During the three and six months ended June 30, 2025, the Company did not enter into any material leases.

Note 16. Related Party Transactions

In the first quarter of 2025, the Company entered into agreements with two entities owned by selling shareholders of Emission (refer to Note 3 - Acquisitions) to continue development work on certain future products for Quanterix. At June 30, 2025, the Company didnot have any open payable balances with these entities and the Company incurred operating expenses of $0.3 million during both the three and six months ended June 30, 2025, respectively.

In the third quarter of 2022, the Company entered into the Harvard License Agreement for certain intellectual property owned by Harvard (refer to Note 15 - Commitments and Contingencies). Harvard is required to pay a portion of the payments received from the Company under the Harvard License Agreement to a member of the Company’s Board of Directors. The same member of the Company’s Board of Directors is also affiliated with Mass General Brigham. Revenue recorded from sales of products and services to Harvard and Mass General Brigham wasnot material and $0.5 million for both the three and six months ended June 30, 2025, respectively, andnot material and $0.5 million for the three and six months ended June 30, 2024, respectively. Cost of product revenue and operating expenses with Harvard and Mass General Brigham werenot material for the three and six months ended June 30, 2025 and 2024, respectively. At June 30, 2025 and December 31, 2024, open payables to Harvard and Mass General Brigham werenot material. Open receivables balances were $0.6 million at June 30, 2025 and werenot material at December 31, 2024.

In the second quarter of 2007, the Company entered into the Tufts License Agreement for certain intellectual property owned by Tufts (refer to Note 15 - Commitments and Contingencies). A member of the Company’s Board of Directors was previously affiliated with Tufts and continues to receive compensation from Tufts on a formulaic basis based on royalties and license payments the Company makes to Tufts. At June 30, 2025 and December 31, 2024, open payable balances to Tufts werenot material.

Note 17. Variable Interest Entities

The Company enters into relationships with, or has investments in, other entities that may be VIEs. The Company assesses the criteria in ASC 810 –Consolidation to determine if any such entities meet the definition of a VIE and require consolidation into its financial statements. Based on the Company’s assessments, it does not have any controlling financial interests in any VIE, and therefore did not consolidate any VIE into its Consolidated Financial Statements during the three and six months ended June 30, 2025 and 2024.

As of June 30, 2025 and December 31, 2024, the carrying value of the Company’s inves tment in a VIE was $0.8 million. Refer to Note 8 - Fair Value of Financial Instruments for the Company’s related valuation disclosures. Maximum exposure to losses related to the VIE is limited to its carrying value and the Company does not have any future funding commitments to the VIE.

Note 18. Segment Reporting

Operating segments are defined as components of an enterprise about which separate discrete information is available for evaluation by the chief operating decision-maker (“CODM”), in deciding how to allocate resources and assess performance. The Company’s CODM is the chief executive officer, who reviews the Company's operations and manages its business as a single operating segment as of June 30, 2025.

The Company’s proprietary digital “Simoa” detection technology is used across all parts of the business to derive revenues through the sale of instruments, consumables, Accelerator Laboratory and LDT services, and warranties. The Company’s accounting policies apply in the same manner across the business.

The Company utilizes consolidated net loss as the measure of segment profitability (loss) as required by ASU 2023-07. The CODM uses this measure, along with the significant revenue and expense lines included in the table below, when analyzing the Company’s operations and performance and determining how to allocate resources. These measures are consistently used by the CODM in comparing budgeted results versus actuals, in determining when or where to invest resources into specific areas of the business, and for decisions on strategic initiatives.

The following table presents the reconciliation of significant segment information reviewed by the CODM to consolidated net loss:

(1)Expenses consist of research and development and selling, general and administrative expenses from the Consolidated Statements of Operations and exclude shipping and handling costs.

(2)Other segment items represent discrete events, non-recurring transactions, or insignificant items that are not used by the CODM to evaluate the Company’s performance or allocate resources, and include:

a. Impairment and restructuring costs – impairment charges for goodwill and other long-lived assets, and costs associated with approved restructuring plans including employee separation costs and any associated costs related to implementing a restructuring plan;

b. Change in fair value of contingent consideration – changes in the fair value of contingent consideration agreements as a result of updated valuation inputs and the passage of time;

c. Other lease costs – amortization of operating lease right-of-use assets and other facility operating expenses from leased facilities the Company is not using;

d. Interest income – interest earned on cash, cash equivalents, and marketable securities, and the accretion of discounts on marketable securities;

e. Other income (expense), net – gains and losses on foreign currency, and other non-recurring items that are not a part of the Company’s core business operations; and

f. Income tax benefit (expense) – income taxes related to federal, state, and foreign jurisdictions in which the Company conducts business.

The CODM reviews usage of cash, cash equivalents, marketable securities, accounts receivable, and inventory as part of evaluating the Company’s performance but does not review or evaluate any other assets.

There have been no changes to the methods used to determine segment profit or loss, or the significant segment captions, across any of the periods presented.

Note 19. Restructuring Costs

On May 12, 2025, the Company announced a plan to reduce operating costs and preserve cash which included a reduction in force. The plan was substantially completed by the end of the second quarter of 2025 and the Company expects to incur costs of approximately $1.5 million.

During the three and six months ended June 30, 2025, the Company incurred expenses of $1.3 million related to the reduction in force, substantially all of which will be cash payments in 2025 for severance and related benefits. These expenses are recorded within impairment and restructuring on the Consolidated Statements of Operations.

The following table shows the accrual activity and payments relating to cash-based restructuring costs for the six months ended June 30, 2025:

The accrual for severance and related benefit costs is included in accrued compensation on the Consolidated Balance Sheets.

Note 20. Subsequent Events

Acquisition of Akoya Biosciences, Inc.

On July 8, 2025 (the “Closing Date”), the Company, completed the transactions contemplated by the Amended and Restated Agreement and Plan of Merger dated as of April 28, 2025 (the “Merger Agreement”), by and among the Company, Wellfleet Merger Sub, Inc., a Delaware corporation and wholly owned subsidiary of the Company (“Merger Sub”), and Akoya Biosciences, Inc., a Delaware corporation (“Akoya”). On the Closing Date, Merger Sub merged with and into Akoya (the “Merger”), with Akoya surviving the Merger as a wholly owned subsidiary of the Company.

Akoya is a life sciences technology company based in Marlborough, Massachusetts delivering spatial biology solutions focused on transforming discovery, clinical research and diagnostics. Spatial phenotyping refers to technology that enables academic and biopharma scientists to detect and map the distribution of cell types and biomarkers across whole tissue samples at single-cell resolution, enabling advancements in understanding of disease progression and patient response to therapy. The acquisition of Akoya is part of the Company's plans to establish the first fully integrated technology ecosystem to identify and measure biomarkers across tissue and blood, expand its technology offerings into oncology and immunology, and expand its portfolio of laboratory service offerings.

Pursuant to the Merger Agreement, at the effective time of the Merger (the “Effective Time”), each share of common stock, par value $0.00001 per share, of Akoya outstanding immediately prior to the Effective Time was converted into the right to receive the following consideration: (a)0.1470 of a fully paid and nonassessable share of common stock, par value $0.001 per share, of the Company (the shares so delivered in respect of each share of Akoya common stock, the “Per Share Stock Consideration”) and, if applicable, cash in lieu of fractional shares, subject to any applicable withholding and (b) $0.37 in cash, without interest (the “Per Share Cash Consideration”). Total consideration paid was approximately 7.8 million shares of Quanterix common stock and $19.6 million of cash.

Concurrently with the acquisition of Akoya, on the Closing Date, the Company paid $82.1 million to settle Akoya's debt financing arrangement with Midcap Financial Trust. The payment included $75.2 million to pay off the principal outstanding and $6.9 million in early termination, legal, and prepayment fees.

The initial accounting for the acquisition was not complete at the time of filing of this Quarterly Report on Form 10-Q due to the timing of the acquisition. As a result, the full disclosures required under ASC 805-10-50 – Business Combinations cannot be made at this time.

In July 2025, the Company announced plans to reduce costs and streamline operations to realize anticipated synergies and other benefits of the Akoya acquisition, which included reductions in force and elimination of duplicate corporate positions. These reductions in force are expected to be substantially completed in the third quarter of 2025. Under these plans, the Company expects to incur expenses of $5.8 million, in addition to the expenses incurred from the May 2025 restructuring (refer to Note 19 - Restructuring Costs), substantially all of which will be cash expenditures incurred in 2025 for severance and related benefits.