Quanterix Corp

Note 11. Stockholders' Equity

The following tables summarize the changes in equity during the three months ended March 31, 2025 and 2024, respectively (amounts in thousands):

Note 12. Stock-Based Compensation

Stock Options

Stock option activity for the three months ended March 31, 2025 is presented below (in thousands, except per share and contractual life amounts):

Restricted Stock Units

Restricted stock unit (“RSU”) activity for the three months ended March 31, 2025 is presented below (in thousands, except per share amounts):

Employee Stock Purchase Plan (“ESPP”)

During the three months ended March 31, 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 March 31, 2025, total unrecognized stock-based compensation expense related to unvested RSUs and stock options was $57.0 million, which is expected to be recognized over the remaining weighted-average vesting period of 2.9 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 12.4% and (1.6)% for the three months ended March 31, 2025 and 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.

Note 15. Commitments and Contingencies

Purchase Commitments

The Company’s 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 March 31, 2025, the Company’s total purchase commitments under these agreements were $1.6 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 months ended March 31, 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 $0.5 million during the three months ended March 31, 2025 and 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 months ended March 31, 2025, the Company did not enter into any material leases.

Note 16. Related Party Transactions

In January 2025, prior to the acquisition of Emission (refer to Note 3 - Acquisitions), the Company entered into agreements with two entities to continue development work on certain future products for Quanterix. The owners of each of these entities were selling shareholders of Emission. At March 31, 2025, the Company did not have any open payable balances with these entities and the Company did not incur any expenses during the three months ended March 31, 2025.

In June 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 March 31, 2025 and December 31, 2024, open payable balances to Tufts werenot material.

In August 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 was $0.3 million for both the three months ended March 31, 2025 and 2024. Cost of product revenue and operating expenses with Harvard and Mass General Brigham werenot material for the three months ended March 31, 2025 and 2024, respectively. At March 31, 2025 and December 31, 2024, open payables to Harvard and Mass General Brigham werenot material. Open receivables balances were $0.6 million March 31, 2025 and werenot material at December 31, 2024.

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 months ended March 31, 2025 and 2024.

As of March 31, 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 March 31, 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. Other lease costs – amortization of operating lease right-of-use assets and other facility operating expenses from leased facilities the Company is not using;

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

c. 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

d. 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, and marketable securities 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. Subsequent Events

Restructuring and Related Costs

On May 12, 2025, the Company announced a plan to reduce operating costs and preserve cash, a part of which will be realized through a reduction in force. The Company expects to incur expenses of approximately $1.5 million related to the reduction in force, substantially all of which will be cash expenditures incurred in 2025 for severance.

Agreement to Acquire Akoya Biosciences, Inc.

On January 9, 2025, the Company entered into an Agreement and Plan of Merger (the “Original Merger Agreement”) with Akoya Biosciences, Inc., a Delaware corporation (“Akoya”), and Wellfleet Merger Sub, Inc., a Delaware corporation and wholly owned subsidiary of Quanterix (“Merger Sub”), to acquire Akoya. Akoya is based in Marlborough, Massachusetts and is a life sciences technology company 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 transaction 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 lab service offerings.

Under the Original Merger Agreement, each share of common stock, par value $0.00001 per share, of Akoya (the “Akoya Common Stock”) outstanding immediately prior to the merger was to be converted into the right to receive 0.318 (the “Original Exchange Ratio”) of a fully paid and nonassessable share of common stock, par value $0.001 per share, of the Company (the “Quanterix Common Stock”) and, if applicable, cash in lieu of fractional shares. In addition, each restricted stock unit in respect of shares of Akoya Common Stock (“Akoya RSUs”) and each option to acquire shares of Akoya Common Stock (“Akoya Options”) that was outstanding immediately prior to the merger was to be automatically converted into a number of restricted stock units and options to acquire shares of Quanterix Common Stock, respectively, based on the Original Exchange Ratio.

On April 28, 2025, the Company, Merger Sub and Akoya, entered into an Amended and Restated Agreement and Plan of Merger (the “A&R Merger Agreement”) that amends and restates the Original Merger Agreement in its entirety, pursuant to which, Merger Sub will merge with and into Akoya (the “Merger”), with Akoya surviving as a wholly owned subsidiary of the Company. Under the A&R Merger Agreement, at the effective time of the Merger (the “Effective Time”), each share of Akoya Common Stock outstanding immediately prior to the Effective Time will be converted into the right to receive (a)0.1461 (the “Exchange Ratio”) of a share of Quanterix Common Stock (the “Per Share Stock Consideration”) and, if applicable, cash in lieu of fractional shares, and (b) $0.38 in cash, without interest (the “Per Share Cash Consideration” and, together with the Per Share Stock Consideration, the “Per Share Merger Consideration”).

Under the A&R Merger Agreement, immediately prior to the Effective Time:

•Each Akoya RSU that is outstanding and unvested (each, a “Rollover RSU”) will automatically be converted into the right to receive the Per Share Merger Consideration upon vesting. Each Rollover RSU shall otherwise remain subject to the same terms and conditions, including vesting, as were applicable immediately prior to the Effective Time.

•Each Akoya RSU that is outstanding and vested immediately prior to the Effective Time will receive the Per Share Merger Consideration.

•Each Akoya Option that is outstanding will, if unvested, become vested, and (a) if the per share exercise price is equal to or greater than the value of the Per Share Merger Consideration, will automatically terminate and be cancelled for no consideration; and (b) if the per share exercise price is less than the value of the Per Share Merger Consideration, will automatically terminate and be cancelled in consideration for the right to receive the Per Share Merger Consideration in respect of a number of shares of Akoya Common Stock determined assuming a synthetic cashless exercise of such Akoya Options as determined based on the aggregate excess of the per share exercise price of such Akoya Options divided by the value of the Per Share Merger Consideration.

The A&R Merger Agreement provides that, (i) the aggregate number of shares of Company Common Stock to be issued by the Company pursuant to the Merger (including shares issuable vesting of Rollover RSUs after the Effective Time) will not exceed 19.99% of the issued and outstanding shares of Company Common Stock immediately prior to the Effective Time and (ii) the aggregate cash consideration to be paid by the Company (including cash payable upon vesting of Rollover RSUs after the Effective Time) will not exceed $20.0 million. If any of such limits were to be exceeded, the Exchange Ratio and the Per Share Cash Consideration, as the case may be, would be reduced, with a corresponding increase in the other component (to the extent such increase does not exceed the limitations described in the foregoing sentence).

The closing of the Merger is subject to a number of conditions, including: (i) approval of the Merger by Akoya stockholders; (ii) the effectiveness of the registration statement on Form S-4 filed with the SEC in connection with the Merger (after the filing of any required post-effective amendment as may be necessary in order to reflect the revised terms of the Merger as contemplated in the A&R Merger Agreement); (iii) the absence of any order issued or entered, or any law enacted or promulgated having the effect of restraining, enjoining, making illegal or otherwise prohibiting the consummation of the Merger; (iv) the Company's submission to Nasdaq of a notification of shares of the Company Common Stock to be issued in connection with the Merger; (v) performance by each party of its respective obligations under the A&R Merger Agreement; and (vi) the absence of a material adverse effect with respect to each of Akoya and Quanterix.

Securities Purchase Agreement

On April 2, 2025, the Company and Akoya entered into a securities purchase agreement, as amended on April 28, 2025 (the “Securities Purchase Agreement”) with Akoya, pursuant to which Akoya will issue and sell to the Company from time to time, in a private placement, one or more convertible promissory notes having an aggregate principal amount of up to $30.0 million (the “Convertible Notes”). Akoya may draw on the Convertible Notes between June 15, 2025 and the earlier of (a) the closing of the Merger and (b) August 31, 2025 if the A&R Merger Agreement is lawfully terminated pursuant to its terms on or prior to such date; provided, however, that if the closing of the Merger occurs on or prior to June 15, 2025, Akoya may not draw on the Convertible Notes.

Any Convertible Notes issued under the Securities Purchase Agreement will mature on the earliest to occur of (i) the 91st day following the earlier of (a) November 1, 2027 and (b) the date that Akoya’s indebtedness under the Credit and Security Agreement, dated October 27, 2020, by and among Akoya, Midcap Financial Trust, as a lender and as agent (“MidCap”), and the other lenders named therein (the “Akoya Existing Loan Agreement”) is repaid in full and all commitments under such documents have been terminated and (ii) subject to the terms of the Subordination Agreement (as defined below), any acceleration of the Convertible Notes. Any Convertible Note issued under the Securities Purchase Agreement will bear interest at a rate per annum equal to the SOFR interest rate plus an applicable margin specified in the Convertible Note to, but excluding, the date of repayment or conversion of the Convertible Note. Interest on the Convertible Notes will be paid in arrears on the first day of each month and on the maturity date of the Convertible Notes. Subject to the terms of the Subordination Agreement, any interest payments will be made exclusively to the Company in cash.

If drawn, the Convertible Notes will be convertible at the election of the Company during the period beginning on the date, if any, that the A&R Merger Agreement is terminated and ending on the maturity date of the Convertible Notes into shares of Akoya Common Stock, at a conversion price based on the Exchange Ratio and the volume weighted average price of the Quanterix Common Stock for the 10 consecutive trading days ending on the trading day prior to the entry into the A&R Merger Agreement, subject to adjustment.

The Convertible Notes prohibit conversion if it would result in the issuance of more than 19.99% of Akoya Common Stock in the aggregate prior to obtaining stockholder approval. The Convertible Notes will also contain customary anti-dilution provisions to adjust the conversion price from time to time based upon certain issuances of securities by Akoya. The Securities Purchase Agreement contains customary representations and warranties and events of default as well as certain operating covenants applicable to Akoya until the closing of the transaction contemplated by the Merger.

Registration Rights Agreement

At such time as Akoya draws any funds and thereby issues any Convertible Notes, Akoya and the Company will enter into a registration rights agreement, pursuant to which, among other things, Akoya must prepare and file with the SEC no later than August 13, 2025 a registration statement with respect to the resale of shares of Akoya Common Stock issuable upon conversion of the Convertible Notes.

Subordination Agreement

At such time as Akoya draws any funds and thereby issues any Convertible Notes, the Company, Akoya and MidCap will enter into a subordination agreement (the “Subordination Agreement”), pursuant to which the Company and Akoya will agree, among other things, that the Convertible Notes will be subordinate to any debt outstanding and obligations owing under the Akoya Existing Loan Agreement.