Quanterix Corporation

ITEM 1A. RISK FACTORS

Our business is subject to risks and events that, if they occur, could adversely affect our financial condition, results of operations, or the price of our common stock. In addition to the other information set forth in this Quarterly Report on Form 10-Q, you should carefully consider the risk factors described in the section titled Part I, Item 1A. Risk Factors in Amendment No. 1 to our Annualour Annual Report on Form 10-K for the year ended December 31, 2024, as filed with the SEC on March 17, 2025. Those risk factors are not the only risks we face. Additional risks and uncertainties not currently known to us or that we deem to be not material also may adversely affect our business, financial condition, and results of operations.

As of the date of this Quarterly Report on Form 10-K/A for tQ, there were no material changes to the risk factors described in our Form 10-K, except for the following changes:

(i) The following new risk factor is added:

We may fail to achieve the expected cost savings and related benefits from our May 2025 cost reduction actions, and the consequences of those actions may adversely impact our business.

On May 12, 2025, we announced a plan to reduce operating costs by approximately $15 million in 2025, with annualized savings of $30 million or 15% of our cost base. Approximately $9 million of the $15 million savings will be realized from headcount actions. We expect to incur expenses of approximately $1.5 million related to the year ended December 31reduction in force, substantially all of which will be cash expenditures incurred in 2025 for severance. There is no guarantee that these cost reduction actions will result in the anticipated savings or other economic benefits, and we may incur unanticipated charges or make payments that were not previously contemplated. Additionally, these actions:

may result in the loss of institutional knowledge and expertise;

may disrupt or restrain the scope of our business activities; and

may make it more difficult to attract and retain qualified personnel, whose duties may be expanded to include those of employees whose positions were eliminated in the reduction-in-force.

If we are unable to realize the anticipated benefits from the reduction-in-force, or if we experience significant adverse consequences from the reduction-in-force, our business, financial condition, and results of operations may be materially adversely affected.

(ii) The risk factor titled Changes in U.S. government policies, including increased tariffs and potential reductions in federal research funding could adversely affect our business. is deleted and replaced in its entirety by the following risk factor:

Changes in U.S. government policies, including reductions in federal research funding and increased tariffs, are adversely affecting our business, though the full extent of the impact is uncertain.

The U.S. government has suspended or withheld disbursement of funds under certain federal research grants (or certain components of grants) and curtailed the grant of new awards, including funding and grants from the National Institutes of Health (NIH). These actions are negatively impacting spending within our industry and causing uncertainty, which is adversely impacting our business and our financial outlook for 2025. Certain of our customers, including academic institutions and research organizations, may depend in whole or in part on federal grants to advance their medical

41

research activities. Any prolonged suspensions or reductions in such funding could slow innovation, delay collaborations, and limit the adoption of new technologies that contribute to our business growth.

Other recent policy actions, including the imposition of new tariffs on imported materials and goods from certain foreign countries, may also have an adverse impact on our business. The U.S. government has announced and/or implemented significant new tariffs on imports from a number of countries, resulting in retaliatory tariffs by certain countries. Increased tariffs on materials, goods and components used by us or our suppliers will likely raise production costs and could disrupt the supply chain. Because tariffs will likely increase the costs of materials, goods and components, we expect we will need to absorb the costs in some cases and/or increase the prices of certain of our products. This could adversely impact demand for our products and our competitive positioning.

If these or similar policy changes continue or expand, we may face increased costs and demand for our products could be impacted. Though the risks referenced above have already adversely impacted our business to some extent, the full impact of funding actions and tariffs on us and on our business partners remains highly uncertain and volatile. We cannot predict the full extent of these impacts, but any prolonged disruption could further adversely affect our business, financial condition, and results of operations.

(iii) The risk factor titled Defects or other quality issues in our products could lead to unforeseen costs, product recalls, adverse regulatory actions, negative publicity, and litigation, including product liability claims, any of which could cause customers to decide not to purchase our products, harm our reputation, and negatively affect our sales, operating results and financial condition. is deleted and replaced in its entirety by the following risk factor:

Defects or other quality issues in our products could lead to unforeseen costs, product recalls, adverse regulatory actions, negative publicity, and litigation, including product liability claims, any of which could cause customers to decide not to purchase our products, harm our reputation, and negatively affect our sales, operating results and financial condition.

Our Simoa products are complex and may contain undetected errors or defects, especially when first introduced or as new versions or new products are released. We have in the past devoted, and will continue to devote, funding and resources to technology development, quality assurance and manufacturing initiatives designed to ensure or improve quality, such as the assay redevelopment program which was initiated in 2023, as filed with the 2 and substantially completed in the fourth quarter of 2023. However, there can be no assurance that we will be successful in our efforts to manufacture products at a level of quality necessary for our customers or to avoid our products containing undiscovered defects or quality issues. Additionally, reduction in personnel who service our instruments may result in service delays, instrument downtime and customer dissatisfaction. Defects, errors or quality issues in our products may discourage customers from purchasing our products and could harm our reputation. We may also be subject to warranty claims and litigation involving claims for damages or incur additional costs, in each case due to errors or defects in our products. In addition, if we do not meet industry or quality standards, if applicable, our products may be subject to recall. A material liability claim, recall or other occurrence that harms our reputation or decreases market acceptance of our products could harm our business and operating results.

Use of our products or services by us or a customer for diagnostic purposes could result in a product liability claim alleging that one of our products contained a design or manufacturing defect that resulted in the failure to adequately perform, leading to death or injury. A product liability claim could result in substantial damages and be costly and time- consuming to defend, either of which could materially harm our business or financial condition. We cannot guarantee that our product liability insurance would adequately protect our assets from the financial impact of defending a product liability claim. Any product liability claim brought against us, with or without merit, could increase our product liability insurance rates or prevent us from securing insurance coverage in the future.

(iv) The risk factors under the heading Risks Relating to the Merger are deleted and replaced in their entirety by the following:

Risks Relating to the Merger

The Merger may not be completed and the AR Merger Agreement may be terminated in accordance with its terms.

The Merger is subject to a number of conditions that must be satisfied (or waived, to the extent permitted), including (i) receipt of the approval of the Merger by Akoya stockholders; (ii) the effectiveness of the registration

42

statement on Form S-4 filed with the SEC on December 23, in connection with the Merger, as amended by any post-effective amendment; (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 submission by us to Nasdaq of a notification of shares of our common stock to be issued in connection with the Merger; (v) performance by each party of its respective obligations under the AR Merger Agreement; and (vi) the absence of a material adverse effect with respect to each of Akoya and us. These conditions to the completion of the Merger, some of which are beyond our control, may not be satisfied or waived in a timely manner or at all, and, accordingly, the Merger may be delayed or not completed. Additionally, either we or Akoya may terminate the AR Merger Agreement under certain circumstances, subject to the payment of a termination fee of $2.6 million by Akoya to us in certain cases. We have incurred and will incur costs in connection with entering into the Original Merger Agreement and the AR Merger Agreement and consummating the Merger, many of which will be payable by us whether or not the Merger is completed. Even if the AR Merger Agreement is terminated under circumstances that would require Akoya to pay us a $2.6 million termination fee, it would not cover all of the expenses and costs we have incurred.

Failure to complete the Merger could negatively impact our future business and financial results and the trading price of our common stock.

If the Merger is not completed for any reason, our ongoing business may be adversely affected and, without realizing any of the expected benefits of having completed the Merger, we would be subject to a number of risks, including the following:

we may experience negative reactions from the financial markets, including negative impacts on our stock price;

we may experience negative reactions from our customers, service providers, partners, vendors, suppliers and employees;

it could negatively impact our ability to achieve future growth, expand our addressable market and achieve scale and profitability on expected timelines;

we will have incurred substantial costs towards completion of the Merger and will generally be required to pay our costs relating to the Merger, such as financial advisory, legal, strategic advisory, accounting costs and associated fees and expenses, whether or not the Merger is completed;

we may provide up to $30 million in bridge financing to Akoya in the form of the Convertible Notes, which would be subordinated to Akoyas existing credit facility, and if the Merger is not completed for any reason, Akoya may not have the financial resources to repay the bridge financing when due, or at all; and

we will have committed substantial time and resources to matters relating to the Merger (including integration planning) which would otherwise have been devoted to day-to-day operations and other opportunities that may have been beneficial to us as an independent company.

Actions of activist or dissident stockholders could negatively affect our business and operations.

Recently two of our stockholders have indicated that they oppose the Merger. In addition, on March 3, 20245, one of these stockholders announced that it had nominated three directors for election to our Board of Directors at our 2025 annual meeting of stockholders. As a result of these actions, we will incur significant expenses even if we are successful in completing the Merger or we are successful in a potential proxy contest.

Perceived uncertainties as to our future direction, strategy, or leadership, and the diversion of management's and our board of director's attention and resources from our business, created by such activism may result in the loss of business opportunities and make it more difficult to complete strategic transactions or attract and retain investors, customers, employees, and other business partners. Such stockholder activism may also cause significant fluctuation in our stock price based on temporary or speculative market perceptions or other factors that do not necessarily reflect the underlying fundamentals and prospects of our business. We cannot predict the outcome or timing of any matters relating to stockholder activism or potential proxy contests or the ultimate impact that such matters may have on our business, liquidity, financial condition, or results of operations.

43

The (issuance of shares of our common stock to Akoya stockholders in connection with the Merger may cause the market price of our common stock to decline.

Upon completion of the Merger, Akoya stockholders will receive (a) 0.1461 (the Amended Annual Report on Form 10-K/A). Those risk factorsExchange Ratio) shares of our common stock (the Per Share Stock Consideration) and (b) $0.38 in cash (the Per Share Cash Consideration and, together with the Per Share Stock Consideration, the Per Share Merger Consideration) for each share of Akoya common stock they hold. In addition, immediately prior to the Merger:

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 prior to the Merger.

Each Akoya RSU that is outstanding and vested immediately prior to the Merger 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 for the shares underlying such Akoya Option 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 for the shares underlying such Akoya Option 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 (each, a "Settled Option").

Based on 49,875,399 shares of Akoya common stock outstanding as of April 25, 2025 and 842,000 Akoya RSUs expected to be vested immediately prior to the Merger and the Exchange Ratio, it is expected that we will issue approximately 7,409,812 shares of our common stock upon the closing of the Merger. Based on 1,254,395 Rollover RSUs outstanding as of April 25, 2025 and the Exchange Ratio, it is expected that Quanterix will issue approximately 183,267 Quanterix RSUs to holders of Rollover RSUs in connection with the Merger. Based on an assumed per share merger consideration value of $1.24 (determined based on an assumed average price per share of our common stock as set forth in the AR Agreement), there would be 1,155,948 shares of Akoya common stock underlying Settled Options, and we would be required to issue and deliver an aggregate of 168,884 shares of our common stock in respect of such Settled Options. Former Akoya stockholders may decide not to hold the shares of our common stock that they will receive in the Merger, and our stockholders may decide to reduce their investment in Quanterix as a result of the changes to our investment profile as a result of the Merger. Both the issuance of this amount of new shares in the Merger and any subsequent sales of these shares may cause the market price of our common stock to decline.

After the Merger, our stockholders will have a reduced ownership and voting interest in Quanterix and may not realize a benefit from the Merger commensurate with their ownership dilution.

The Merger will dilute the ownership position of our stockholders and result in Akoya stockholders having an ownership stake in Quanterix. Based on the number of shares of our common stock and Akoya common stock outstanding as of May 1, 2025, upon completion of the Merger, our current stockholders are not the onexpected to own approximately 84% of our outstanding common stock and former Akoya stockholders are expected to own approximately risks we face.16% of our outstanding common stock immediately following the closing of the Merger.

If Quanterix and Akoya as a combined company (the Combined Company) is unable to fully and timely realize the strategic and financial benefits currently anticipated from the Merger, our stockholders will have experienced substantial dilution of their ownership interests without receiving any commensurate benefit, or only receiving part of the commensurate benefit to the extent the Combined Company is able to realize only part of the strategic and financial benefits currently anticipated from the Merger.

44

Until Additional risks and uncertthe completion of the Merger or the termination of the AR Merger Agreement pursuant to its terms, we are prohibited from entering into certain transactions and taking certain actions that might otherwise be beneficial to us and our stockholders.

From and after the date of the Original Merger Agreement and prior to the completion of the Merger or the termination of the AR Merger Agreement pursuant to our terms, we are restricted from taking specified actions without the consent of Akoya and are required to conduct our business in the ordinary course, subject to certainties not currently known to us or that  exceptions. These restrictions may prevent us from taking actions during the pendency of the Merger that would have been beneficial. Adverse effects arising from these restrictions during the pendency of the Merger could be exacerbated by any delays in the completion of the Merger or termination of the AR Merger Agreement.

Obtaining required approvals and satisfying closing conditions may prevent or delay completion of the Merger.

The Merger is subject to a number of conditions to closing. No assurance can be given that the required Akoya stockholder approval can be obtained or that the required conditions to closing will be satisfied, and, if all required approvals are obtained and the required conditions are satisfied, no assurance can be given as to the terms, conditions and timing of such approvals. Any delay in completing the Merger could cause the Combined Company not to realize, or to be delayed in realizing, some or all of the benefits that we deem to be not material also expect to achieve if the Merger is successfully completed within our expected time frame. Additionally, any delays in satisfaction of the closing conditions will increase the length of time that we are subject to certain restrictive covenants under the AR Merger Agreement during the pendency of the Merger and increases the risk of disruptions to our operations and business relationships and the impediments to our ability to pursue certain business opportunities or strategic initiatives, which may adin turn cause the Combined Company to not realize some or all of the expected benefits of the Merger or adversely affect our business, financial condition, and results impact our future financial and strategic conditions on a standalone basis if the required approvals and conditions to closing are not obtained or satisfied.

Failure to attract, motivate and retain executives and other key employees could diminish the anticipated benefits of the Merger.

The success of the Merger will depend in part on our ability to retain the talent and dedication of key employees of each company. It is possible that these employees may decide not to remain with us or Akoya, as applicable, while the Merger is pending, or with the Combined Company following consummation of the Merger. If key employees of either company terminate their employment, or if an insufficient number of employees or sales representatives are retained to maintain effective operations, the Combined Companys business activities may be adversely affected and managements attention may be diverted from successfully integrating Quanterix and Akoya to hiring suitable replacements, all of operawhich may cause the Combined Companys business to suffer. In additions.

As of , we and Akoya may not be able to locate suitable replacements for any key employees that leave either company or offer employment to potential replacements on reasonable terms. Moreover, there could be disruptions to or distractions for the workforce and management, including disruptions associated with integrating employees into the Combined Company. No assurance can be given that the Combined Company will be able to attract or retain key employees to the same extent that those companies have been able to attract or retain their own employees in the past.

The Merger, and uncertainty regarding the Merger, may cause our customers, service providers, partners, vendors, suppliers and other business relationships to delay or defer decisions and adversely affect our ability to effectively manage our business, which could adversely affect our business, operating results and financial position and, following the completion of the Merger, the Combined Companys business, operating results and financial position.

The Merger will happen only if certain stated conditions are met. Accordingly, there may be uncertainty regarding the completion of the Merger. This uncertainty may cause existing or prospective customers, service providers, partners, vendors, suppliers and other business relationships to delay or defer othe date or decisions, including entering into contracts or making other decisions, or seek to change or cancel existing business relationships. Additionally, we are subject to certain restrictive covenants under the AR Merger Agreement during the pendency of this Quarterly e Merger that may (i) cause us to delay or defer other decisions including entering into contracts or arrangements with existing or prospective customers, service providers, partners, vendors, suppliers and other business relationships or (ii) inhibit our ability to take advantage of certain business opportunities or strategic initiatives. Any such disruptions such as delays or deferrals of those decisions or changes in existing agreements could adversely affect our business, operating results and financial position, whether the Merger is ultimately completed, and following the completion of the Merger, the Combined Company, including an adverse effect on the Combined Companys ability to realize the anticipated synergies and other benefits of the Merger.

45

The risk, and adverse effect, of any such disruptions could be exacerbated by a delay in completion of the Merger or termination of the AReport on Form 10-Q Merger Agreement.

Whether or not the Merger is completed, the announcement and pendency of the Merger could cause disruptions in our business, which could have an adverse effect on our business and financial results.

Whether or not the Merger is completed, the announcement and pendency of the Merger could cause disruptions in our business, including by diverting the attention of our management and employee team, such as those involved in day-to-day operations, there were no material changes to toward the completion of the Merger. In addition, we have diverted significant management resources in an effort to complete the Merger and are each subject to restrictions contained in the AR Merger Agreement on the conduct of our business. If the Merger is not completed, we will have incurred significant costs, including the diversion of management resources, for which we will have received little or no benefit.

We expect to incur substantial costs related to the risk factors describeMerger and integration.

We have incurred and expect to incur substantial non-recurring costs associated with combining the operations of the two companies, as well as transaction fees and other costs related to the Merger. Such costs include, among others, filing and registration fees with the SEC, and legal, accounting, investment banking, consulting and public relations fees. Most of these costs are payable by us regardless of whether the Merger is completed.

There will also be restructuring and integration costs incurred in connection with the Merger. There are processes, policies, procedures, operations, technologies and systems that must be integrated in our Aconnection with the Merger and the integration of Akoyas business into the Combined Company. Although we expect that the elimination of duplicative costs, strategic benefits and additional income, as well as the realization of other efficiencies related to the integration of the businesses, may offset incremental transaction expenses, Merger-related and restructuring costs over time, any net benefit may not be achieved in the near term or at all. While we have assumed that certain expenses would be incurred in connection with the Merger and the other transactions contemplated by the AR Merger Agreemended Annual Report t, there are many factors beyond our control that could affect the total amount or the timing of the integration and implementation expenses.

Lawsuits or other legal proceedings may be filed against us, Akoya, the Combined Company and members of their respective boards of directors and management, and have been filed against Akoya and its directors and management already, in connection with the Merger, and an adverse ruling in any such lawsuit may prevent the Merger from becoming effective or from becoming effective within the expected time frame, or have an adverse impact on the Combined Companys business and operations.

Transactions such as the Merger are frequently subject to litigation or other legal proceedings, including actions alleging that our board or Akoyas board breached their respective fiduciary duties to their stockholders by entering into the AR Merger Agreement, by failing to obtain a greater value in the transaction for their stockholders or otherwise. Neither we nor Akoya can provide assurance that such litigation Form 10-K/A.or other legal proceedings will not be brought. If litigation or other legal proceedings are in fact brought against us or Akoya, or against our board or Akoyas board, they will defend against it, but might not be successful in doing so. An adverse outcome in such matters, as well as the costs and efforts of a defense even if successful, could have a material adverse effect on the business, results of operation or financial position of Quanterix, Akoya or the Combined Company, including through the possible diversion of either companys resources or distraction of key personnel.

Furthermore, one of the conditions to the completion of the Merger is the absence of an order (whether temporary or permanent) issued or entered after the date of the AR Merger Agreement by any governmental body enjoining or otherwise prohibiting the consummation of the Merger. As such, if any plaintiffs are successful in obtaining an injunction preventing the consummation of the Merger, that injunction may prevent the Merger from becoming effective or from becoming effective within the expected time frame.

If the Merger is completed, the Combined Company may be exposed to increased litigation or other legal proceedings from stockholders, customers, partners, suppliers, contractors and other third parties due to the merger of our and Akoyas businesses following the Merger. Even if such lawsuits or other legal proceedings are without merit, defending against these claims can result in substantial costs and divert management time and attention. Such litigation or an adverse judgment resulting in monetary damages may have an adverse impact on the Combined Companys business and results of operations or may cause disruptions to its operations.

46