Deep Tissue Imaging (Phase 2)

The Phase 2 RFA is a two-step application process. We invite letters of intent (LOI) where applicants will provide a short proposal detailing the current state of a deep tissue imaging technology and how their project will advance this technology. A subset of the LOI applicants will be invited to submit a full application for four-year projects.

To accelerate recent innovations in deep tissue imaging technology development, this Phase 2 RFA is open to all applicants, as detailed in the Eligibility section below. Phase 2 is not limited to Deep Tissue Imaging Phase 1 pilot projects or investigators. Applications from Phase 1 pilot project grantees may 1) continue development of their Phase 1 project, 2) modify or expand the scope of their Phase 1 project, or 3) propose a new project.

Scientific Scope

The long-term goal of this opportunity is to drive technology development aimed at visualizing cellular structure and function throughout the body. We especially seek proposals that support the development of tools for visualizing cellular-level processes in deep tissue. This funding opportunity is explicitly aimed at technology development. It is not intended to support question-driven basic or translational research, clinical trials, or drug development.

Examples of research themes:

• Adaptive optics for deep tissue imaging
• Bioacoustic probe, hardware, and/or method development
• Biomagnetic probe, hardware, and/or method development
• Biochemical probe or method development
• Multi-photon hardware or method development
• Quantum technologies for deep tissue imaging
• Deep tissue imaging techniques with potential applicability to the human body

We particularly encourage applications from:

• Researchers in disciplines outside of biomedicine who bring new technology, resources, or frameworks to studying cellular processes;
• Women, those underrepresented or marginalized in science, and diverse groups worldwide; and
• Early career investigators, defined as principal investigators who have been in an independent faculty role for less than six years at the time of application, i.e. starting after July 11, 2017.

Desired Outcomes

Successful outcomes for this RFA could include:

• Development of biological probes to label cells and subcellular processes throughout the body;
• Development of technologies that enable imaging at cellular resolution anywhere in complex living organisms; or
• Development of new computational techniques and algorithms for relevant signal extraction and analysis.

Collaboration and Open Science

CZI seeks investigators who will contribute to a collaborative interdisciplinary network and the advancement of the deep tissue imaging field.

• Investigators and members of their labs will participate in annual meetings of all funded groups, smaller meetings focused on specific biological or technical topics, and regular webinars.
• Investigators and CZI staff will work together to identify resources and technology that can drive the imaging field forward.
• Investigators will commit to rapid dissemination of all resulting data, protocols, code, reagents, and results prior to publication through resources such as protocols.io, GitHub, Addgene, and preprints. Please see the Policies section for additional details.

Given the length of the award, an engagement and dissemination plan is required. While technology development should be the primary focus of a proposal, validation and dissemination for broader application of the developed products must also be addressed. Co-PIs whose roles on teams focus on validation and dissemination are permissible.

• Eligibility is not limited to CZI Deep Tissue Imaging Phase 1 grant awardees. 
• Applications may be submitted by domestic and foreign nonprofit and for-profit organizations, public and private institutions, such as colleges, universities, hospitals, laboratories, units of state and local government, companies, and eligible agencies of the federal government. As part of the application process, for-profit organizations may need to provide additional information on the charitable purposes of the proposal. Grants are not permitted to individuals, only to organizations.
• There may be more than one application submitted by each organization.
• Each application should designate one Principal Investigator (PI) as the Coordinating Principal Investigator (Coordinating PI). The Coordinating PI will act as the administrative contact between CZI and all PIs on the grant (Co-PIs). The Coordinating PI must submit the application on behalf of all PIs. The Coordinating PI must be affiliated with the institution submitting the application, and grant funds will be awarded to that institution, which will take responsibility for distributing funds to any other institutions. Note that institutions outside the U.S. may not subcontract to U.S. institutions, so please be mindful when selecting the Coordinating PI/institution.
• Each application should have a minimum of one PI (Coordinating PI), but may designate up to six total PIs (one Coordinating PI and up to five Co-PIs).
• PIs may only serve as the Coordinating PI on one application, but may serve as a Co-PI on applications different from the one they submitted.
• Co-PIs may serve as a Co-PI on multiple applications.
• PIs/Co-PIs on one application may be employed at the same or at different institutions. 
• PIs and Co-PIs must hold a PhD, MD, or equivalent degree.
• PIs and Co-PIs must each run laboratories in which they control their budget, their space, and their research. Independence in an academic setting is typically demonstrated by a full-time faculty appointment, a tenure-track position, allocated space, a start-up package, and institutional commitment as defined or verified in a letter from a department chair or equivalent. Independence may be defined differently in other organizations. Note: an upload of the letter or proof of independence is not required at the time of application.
• CZI encourages applications from underrepresented populations, women, and early-career scientists.
• Meta employees, including employees of any subsidiary Meta entities, as well as employees of Chan Zuckerberg Initiative, LLC, are not permitted to apply.
• CZI reserves the sole right to decide if an applicant and applicant organization meet the eligibility requirements.
• CZI reserves the right to request budget changes prior to award.
• We welcome applications from any country, provided the proposed work is compliant with the United States Treasury Department’s Office of Foreign Asset Control (OFAC) sanctions program. Prior to award, all grant applications will be reviewed for compliance with the United States Treasury Department’s Office of Foreign Asset Control (OFAC) sanctions program, the United States Department of Commerce’s export administration regulations, the Foreign Corrupt Practices Act (FCPA), any other applicable U.S. laws and regulations, and any corresponding laws and regulations in the country where the applicant is based. All grant agreements will also require the grantee to comply with these laws and regulations. For additional information please refer to: the U.S. Treasury Department’s resources, the International Trade Administration’s website on US Export Controls, and the Department of Justice’s website on the FCPA. 
• While applicants from all countries are welcome to apply, because of required ongoing compliance with U.S. sanctions and export controls, an applicant’s funding eligibility may need to be reassessed if the applicable laws and regulations change at any time. As a result, even if an applicant is eligible to receive funding at the time the application is reviewed, the applicant’s status may change later in the process or during the course of the grant term.

CZI suggests that you consult your home institution to determine eligibility to apply for this grant and your institutional policy on indirect costs. For questions about eligibility for this award or the application process, please contact us in advance of the proposal deadline at sciencegrants@chanzuckerberg.com. Deadline extensions will not be granted.

The Chan Zuckerberg Initiative uses SurveyMonkey Apply (SMApply) as its grants management portal. All applications must be submitted through this portal (https://apply.chanzuckerberg.com). SMApply is configured to work best using the Google Chrome browser. It is recommended that you familiarize yourself with this portal well in advance of any deadlines. Deadline extensions will not be granted.

Application specifics

• The application process is a two-stage process: Letter of Intent (LOI) and Full Application (if invited). 
• Eligibility: Please refer to the Eligibility section of the announcement.
• Award Period: Awards will be four years (48 months) in duration with an expected start date of March 1, 2024.
• Budget: A budget limit has not been set on a per project basis to account for the different resourcing levels likely required by hardware, software, and protocol development projects that may be supported by this RFA. While an upper budget limit has not been set, requests larger than $2.5 million USD will receive additional scrutiny, and may undergo additional budget adjustments. Proposed budgets should reflect the project scope. Indirect costs cannot exceed 15 percent of direct costs. A detailed budget is not required at the LOI stage.

The application (Letter of Intent) consists of the following sections (called tasks in the grants portal): Applicant Details, Organization Details, Proposal Details, Project Proposal, Biosketches, Equal Opportunity & Diversity (optional).

1. Log into https://apply.chanzuckerberg.com.

2. Click the green View Programs button. Find the program/RFA; you may need to scroll down. Click the green More button.

3. Click the green Apply button in the upper right and complete all sections.

4. Enter the title of your application. Proposal title is limited to 60 characters, including spaces. If you need to edit your proposal title, click on the My Applications link in upper right and click the green Continue button on the application you wish to edit. Once the application page opens, click on the three dots to the right of the application title and select Rename from the dropdown menu. Please note that you will not be able to make changes to the title of your application between the LOI and full proposal period.

5. Task 1: Applicant Details: The information entered should be for the individual submitting the application who will act as the main person responsible for the application and as its point of contact. Please note that this person and organization must remain the same between the LOI and full application (if selected).

• Name and email are auto-filled. To edit your name or email, please do so in your account information by clicking your name in the upper right corner and clicking My Account in the dropdown menu.
• Degree(s).
• Organization, Title/Position, Department or equivalent.
• Career status: Select early-career (faculty 0 to 6 years), mid-career (faculty 6+ to 10 years), or neither. Note: Early- or mid- career status is not required to be eligible for this RFA.
  • Early-Career Definition: In the context of this RFA, an early-career investigator is someone who has been in an independent faculty position (or equivalent) for zero to six years at the time of the LOI application due date, i.e. have started their first independent position between July 11, 2017 and July 11, 2023.
  • Mid-Career Definition: In the context of this RFA, a mid-career investigator is someone who has been in an independent faculty position (or equivalent) for more than six to 10 years at the time of the LOI application due date, i.e. have started their first independent position between July 11, 2013 and July 10, 2017.
• ORCID iD: Enter in format XXXX-XXXX-XXXX-XXXX. ORCID iDs are unique, digital identifiers that distinguish individual scientists and unambiguously connect their contributions to science over time and across changes of name, location, and institutional affiliation. ORCID iDs will be used to streamline reporting in our applications and grant reports to reduce the burden on grantees. For more information, please visit https://orcid.org/register. (Please contact us at sciencegrants@chanzuckerberg.com if you wish to opt out.)

6. Task 2: Organization Details: Complete all fields in this task; all fields are required.

• Type of organization: Academic, Other Nonprofit, Industry/company, Government, or Other. If Industry/company is selected, an additional set of questions will need to be completed in the portal to determine eligibility.
• Organization name/Address/City/State/Country/Website.
• Tax ID: Enter your organization’s Employer Identification Number (EIN), as assigned by the Internal Revenue Service in the 9-digit format (XX-XXXXXXX; 10 characters total). Foreign organizations or others who do not have an EIN should enter 44-4444444.

7. Task 3: Proposal Details: All sections are required.

• Project Title (auto-filled): Project title is limited to 60 characters, including spaces. If you need to edit your proposal title, navigate to your application summary page, click on the three dots to the right of the application title (next to the Preview link) and select Rename from the dropdown menu.
• Project Purpose: Summarize your research project; limited to one sentence. Please use a third-person voice. (maximum of 200 characters including spaces).
• Co-Principal Investigators: Indicate how many Co-PIs in the application. If there are no Co-PIs, enter zero. For applications with Co-PIs, complete the following information for each Co-PI (maximum of five). Do not include the Coordinating PI (applicant) in this section.
  • Co-PI name, Title/Position, Degrees, ORCID iD (format: XXXX-XXXX-XXXX-XXXX), Email, Career status
  • In the context of this RFA, an early-career investigator is someone who has been in an independent position for zero to six years at the time of the LOI application due date, i.e. have started their first independent position between July 11, 2017, and July 11, 2023 and mid-career as someone who has been in an independent position for more than six to 10 years at the time of the LOI application due date i.e. have started their first independent position between July 11, 2013 and July 10, 2017.
  • Organization Name, Country, Website
  • Type of organization (drop-down menu: Academic, Other Nonprofit, Government, Company/industry, Other).
  • Tax ID: Enter the Co-PI organization’s Employer Identification Number (EIN), as assigned by the Internal Revenue Service in the 9-digit format (XX-XXXXXXX; total of 10 characters). Foreign organizations or others who do not have an EIN should enter 44-4444444.

8. Task 4: Project Proposal: Upload your project proposal as a single PDF; font must be 11 point or larger and margins must be at least one-half inch (top, bottom, left, and right) for all pages. Include the following sections:

• Proposal Body: maximum of 500 words
  • Background: Describe the current state-of-the-art technology you are working on.
  • Project Goals: Detail the technology goals of the project.
  • Significance: Describe the scientific significance if the technology goals are met.
  • Project Plan: Describe the research and development strategy to be employed and main milestones.
• Figures (optional): Limited to one page, inclusive of legends. Figure legends do not count towards the word count.
• References Cited in your proposal: No word/page limit; include complete source references.

9. Task 5: Biosketches: Upload the biosketches in PDF format for the Coordinating PI and each Co-PI on the team listed in the Project Details section. Biosketches can be uploaded in a combined single PDF or one PDF for each PI; maximum of five pages per biosketch; NIH format or similar.

10. Task 6: Equal Opportunity & Diversity (optional): CZ Science supports the science and technology that will make it possible to cure, prevent, or manage all diseases by the end of this century. Different communities are affected by or experience disease in different ways. Moreover, due to systemic barriers, the scientific enterprise itself is not a place where all voices and talents thrive. We believe the strongest scientific teams — encompassing ourselves, our grantees, and our partners — incorporate a wide range of backgrounds, lived experiences, and perspectives that guide them to the most important unsolved problems. To enable our work, we incorporate diverse perspectives into our strategy and processes, and we also seek to empower community partners to engage in science.

We request demographic information associated with applications submitted to CZI in response to our open calls. This information helps us learn from the RFA process, as well as improve our strategies to help ensure members of underrepresented or marginalized groups in science are aware of and able to apply to CZI opportunities. Please note that answering the questions below is voluntary, and receiving funding is not contingent on providing this information. Demographic information provided may be used in our grant-making process but will not be used as the sole or determinative factor in our grant funding decisions. We may also publish aggregated data in various public forums, such as a website or blog. All responses will be shared only with limited personnel and service providers, who will use that information only for the purposes described in this paragraph.

If you have any additional questions about why we ask this, what we do with the data, or to share suggestions for improvement, please reach out to sciencegrants@chanzuckerberg.com.

The information below may be entered for the Applicant / Coordinating PI, who will be submitting the application on behalf of the team. The categories listed below may not capture all possible identities; in the event that the categories do not accurately reflect your identities, please use the space provided to self-describe.

• What is your race/ethnicity? (optional)
• What is the year of your last academic degree? (optional)
• What is your gender? (optional)
• Are you transgender? (optional)
• Are you a member of the LGBTQIA+ community? (optional)
• Do you have one or more disabilities? (optional)

The Applicant / Coordinating PI may also provide aggregated information on the demographics of the Co-Prinicipal Investigators (Co-PIs) listed in the Project Details section of the application if those Co-PIs agree to share that information with CZI. The categories listed below may not capture all possible identities; in the event that the categories do not accurately reflect their identities, please use the space provided to describe.

• How many of the Co-PIs self-identify as each of the following genders?
  • Woman, Man, Non-binary/Third gender, Prefer not to state, Prefer to describe (optional)
• How many of the Co-PIs self-identify as each of the following races/ethnicities?
  • Two or More Races, Black and/or African American, Asian, White, Hispanic or Latinx, Middle Eastern or North African, Native Hawaiian or Other Pacific Islander, American Indian or Alaska Native, Prefer not to state, Prefer to describe (optional)

11. Mark all tasks as complete.

12. Submit your application: Once all required tasks are completed, click the green Review & Submit button. Note that once your application has been submitted, it cannot be edited.

• If the Submit button is grayed out, it means your application is not yet complete— check that all required fields are entered and you have clicked the Mark as Complete button within each task.
• Click the green Submit Your Application button on the left side of the window. Confirm your submission by clicking the Submit button in the pop up window.

13. Once your application is submitted, you will receive an email confirming submission. If you do not receive a confirmation email within a few minutes, please check your spam folder. If you still did not receive your confirmation email, please email sciencegrants@chanzuckerberg.com.

FULL APPLICATION

Applicants will be notified by email by August 15, 2023 if they have been invited to submit a Full Application. Detailed application instructions will be provided at that time. The Full Application will require additional materials such as a budget description, biosketches, and a detailed project proposal. Full Applications will require institutional sign-off (see Institutional Approval Form for details), so please be sure that your institution is able to comply with all requirements before submitting a Letter of Intent. Please also review the Full Application submission timeline before submitting a Letter of Intent; deadline extensions will not be granted. Full Applications (if invited) must be submitted by 5 p.m. Pacific Time on September 26, 2023.

QUESTIONS?

For administrative and programmatic inquiries pertaining to this RFA, please contact sciencegrants@chanzuckerberg.com. For technical assistance with SMApply, please contact support@smapply.io or while logged into SMApply, click on the information ”i” link in the upper right corner and submit a help request ticket.

The Chan Zuckerberg Initiative adheres to our core values in both proposal selection and evaluation of progress.

CZI will evaluate all applications for scientific merit through independent expert review. The initial application is a Letter of Intent (LOI) that describes the participants and the technological goals. Selected individuals and groups will be invited to submit a Full Application. Final decisions will be made by CZI staff in consultation with our scientific advisors. There is no expectation of any specific number of awards, and the Chan Zuckerberg Initiative reserves the sole right to not recommend the funding of any applications. CZI does not provide feedback on decisions for unfunded proposals.

Selection of awardees will be based on:

• The quality of the proposal, and the expertise and capacity of the group for addressing the proposed project.
• Significance and potential impact of the project.
• Potential of the awardee to contribute to and benefit from a collaborative interdisciplinary network.

• Funds from this award are intended to support research activities. Grants are made to institutions on behalf of the named award recipients, and reasonable flexibility on how these funds are utilized is allowed, provided that funds are used to support research activities related to the project. A detailed budget is required.
• For awarded projects, financial statements and progress reports will be due at the conclusion of each grant year. Specific deliverable requirements will be outlined in the award notification. Grantees of funded projects will be required to participate in regular meetings, including annual scientist meetings. Travel support for these meetings will be provided by CZI separately from the requested grant funds. 
• Grantees may obtain funds for their research from other funding sources, provided that there is no conflict with meeting the terms of the CZI award.
• Unused research funds may be carried over to the following year, and requests for no-cost extensions will be considered at the end of the overall project period and upon receipt of an annual report.
• Indirect costs cannot exceed 15 percent of direct costs. Indirect costs may not be assessed on capital equipment or subcontracts, but subcontractors may include up to 15 percent indirect costs of their direct costs. Non-charitable entities must include a clear allocation and explanation for any indirect costs included in a proposed budget.
• International grantees must use all grant funds exclusively for activities conducted outside the United States of America. 
• Ethical conduct: CZI advocates the highest standards for the ethical conduct of research. In addition to requirements of their own countries, grantees must adopt procedures for the use of animals in research and for the ethical treatment of human subjects and tissue donors, including obtaining their or their appropriate proxy’s written informed consent. CZI regards the policies of the National Institutes of Health as a strong model for such procedures.
• Data, publication, and dissemination policies:​ To accelerate scientific discovery and collaboration, CZI supports a consent, sharing, and publication policy for open and rapid dissemination of research results, including methods, data and reagents, and a policy for software development that maximizes accessibility, reuse, and shared development. Under rare circumstances, exceptions to the above may be considered where there are specific situations that make meeting these goals impossible or counterproductive to the project.
  • Software code: CZI requires sharing of software code developed by its grantees generally to be made publicly available on GitHub (or a similar public service). All new code must be released under a permissive open source license (MIT, BSD 2-Clause, BSD 3-Clause, or Apache v2.0). All pre-existing and derivative code must be licensed under the most permissive license possible, given the licensing terms of the pre-existing code. All analysis packages must be released through the appropriate language-specific package manager (e.g., PyPi for Python, Bioconductor and CRAN for R) with documentation, example data, and interactive demos (e.g., Jupyter notebooks), and the use of Docker or similar container technologies to ensure portability and reproducibility. Software code supported by CZI must be archived for long-term digital preservation and citability, when applicable. 
  • Content and data sharing: ​CZI is committed to developing and using platforms that disseminate data openly and freely. Any datasets either curated or generated through the proposal must be made as publicly available and easily accessible through an appropriate data repository as legally permissible, when applicable, under an Open Definition conformant license. Ideally data sets would not include personally identifiable information, but if they do, consent to sharing the data must be obtained. Metadata, documentation, and intended use cases, as appropriate, must be made available under an Open Definition conformant license, preferably CC0 or CC BY/CC BY SA for content that requires explicit attribution.
  • Publications:​ To encourage rapid dissemination of results, any publications related to this funded work must be submitted to a preprint server (such as bioRxiv, medRxiv, arXiv, or any appropriate preprint repository), at or before the first submission to a journal. Experimental protocols should be made publicly available through a protocol sharing service, such as protocols.io. CZI requests that scientific publications, preprints, and presentations that result from this award acknowledge support from this funding. 
  • Reagent sharing: Resources and reagents developed with this funding support must be available for rapid dissemination to the community, where possible in an accessible community repository, such as Addgene (for plasmids/DNA reagents/viruses), Jackson Labs (for model systems lines), etc. This requirement applies to cell lines, transgenic organisms, plasmids/clones, antibodies, and other reagents.
  • Consent: All human tissues must be adequately and fully consented to permit maximal sharing of the resulting data and any resulting tools, subject to applicable laws, regulations, or institutional ethical requirements. Any desired exceptions to this policy must be identified at the time of application, and such requests may affect the application’s chance of success. We are aware that there may be circumstances where broad consent may be challenging, and in some cases consent may be subject to alteration or revocation; we encourage investigators to discuss these cases with CZI scientific staff.
  • Intellectual property rights: CZI does not require assignment of ownership to any data, published results, or any other intellectual property that results from the work funded by these grants but will have the same rights generally granted to others. CZI supports and promotes policies that enable results and technologies to have the broadest reach and impact. To this end, all newly developed software must be made available through permissive open source licenses as described more fully above. Other technology and intellectual property rights (such as patents) must be made freely available for all academic and non-commercial use, and where intellectual property rights are commercialized, they must generally be subject to non-exclusive commercial licenses that enable broad availability and dissemination. 
• Applications selected through this process will either be funded by the Chan Zuckerberg Initiative Foundation (CZIF) or recommended for funding through the Chan Zuckerberg Initiative Donor-Advised Fund (DAF) at the Silicon Valley Community Foundation (SVCF).

All submitted applications will be kept confidential, except (1) as necessary for our evaluation or to comply with any applicable laws; and (2) to the extent that the application is made public or available to others without a duty of confidentiality through no fault of CZI. Notwithstanding, successfully funded proposals may be made publicly available and/or shared with other grantees or collaborators. Unfunded proposals will remain confidential as provided herein; however, information, including brief summaries of the proposed projects, project metrics, and the types of organizations that have applied for funding, may be made publicly available in aggregate form. Application materials will not be returned to applicants.