NB644040-25-01645 Statement of Work.pdf

PERFORMANCE WORK STATEMENT

Quantitative, High-Speed, High-Volume Cell Imaging Computer Programming Support

I. BACKGROUND

The National Institute of Standards and Technology (NIST) Biosystems and Biomaterials Division (BBD) of the Material Measurement Laboratory (MML) advances research, knowledge, and applications of biological science with increasingly quantitative tools.

BBD’s mission is to develop and establish confidence in tools and methods that are used to quantitatively characterize cell response and cell products. To carry this out, there exists a need to develop and validate computational methods, data/knowledge mining tools, and semantic approaches for describing and tracking experimental parameters and image data processing steps.

BBD’s activities also respond to industry, consortia, and standards groups’ needs by concentrating on key areas at the forefront of technology and by assisting in the transfer of technology and expertise to industry.

BBD is developing measurement and analytical systems that will lead to better quantification and prediction of complex biological processes for improved drug development, personalized medicine, cell therapies, and the design and manufacturing of cells and cell products for the health, agriculture, and environment sectors.

One of BBD’s most important tools is the quantitative microscopic imaging of living cells over time. With these new quantitative tools, BBD is entering an era of cell biology where it will be possible to understand and predict the complex regulatory mechanisms that determine cell function. With that understanding comes an increased ability to design, control, and manufacture cells. Traditionally, cell biology has been an academic area of research focused on basic science and observational approaches of a semi-quantitative nature.

Biological imaging today is conducted with high-throughput instruments that generate massive amounts of images that serve as raw data for scientific discovery. The sheer volume of images prohibits manual processing and analysis; therefore, computational methods are necessary to automate analysis and enable scientific discovery. Computational and programming techniques are needed to address the challenges related to high-throughput experimentation, including image acquisition and sampling, organizing and processing large datasets, and analyzing and extracting knowledge from massive amounts of data. Bespoke computer code is required to enable these essential functions.

II. PURPOSE

NIST requires computer programs that will enable advanced research and development of BBD’s high-speed, high-volume cell imaging capabilities. Attaining this expertise will enable BBD to provide technical leadership in the development of measurement technologies for cell biology.

NIST’s existing image processing pipeline accommodates large data volumes. Image data on the order of 10 GB in size are collected every two minutes for up to 72 hours of imaging with an in-house Zeiss Axio Observer Z1 light microscope operating with Inscoper control software. As such, some image processing is performed “on the fly” as data are being collected from the microscope with processing steps that may include focal plane selection, image stitching, flat field correction and background subtraction.

Experimental details are captured as metadata in JSON format using existing NIST tools and user interface.

III. SCOPE

The Contractor shall create, evaluate, and integrate multiple capabilities for quantitative image data acquisition, processing, visualization, and analysis.

The Contractor shall provide all support for oversight, administration, and technical execution for this project.

The Contractor shall be responsible for maintaining accurate records of all project activities.

IV. SPECIFIC REQUIREMENTS

Task 1: Enhance Existing Image Processing Pipeline to Include Application of Existing 3D U-Net Code.

The Contractor shall add additional functionality to NIST’s existing automated processing pipeline by adding the application of existing U-Net code that identifies mitosing cells (i.e., cells undergoing mitosis or cell division) based on x,y coordinates and time criteria. This will achieve robust and efficient processing of acquired images and appropriately organized and named image data files. The operation of this code will perform “on the fly” as an additional component to NIST’s existing pipeline.

The Contractor shall:

• Identify the most recent version of existing 3D U-Net code and become familiar with the key variables.

• Run the existing code and ensure that it produces accurate results.

• Document the existing code.

• Integrate the existing code into NIST’s automated pipeline routine and validate functionality of the resulting functionality enhancement.

Task 2: Enhance Existing Image Processing Pipeline with Tracking Routine Integration

The Contractor shall add additional functionality to the automated processing pipeline by adding the application of an existing NIST algorithmic routine to track cell objects in subsequent time frames. This addition will achieve robust and efficient processing of acquired images and appropriate organized and named image data files. The operation of the code will perform “on the fly” as an additional component to NIST’s existing pipeline.

The Contractor shall:

• Identify the most recent version of the existing code and become familiarized with the key variables.

• Run the existing code and ensure that it produces accurate results.

• Document the existing code.

• Integrate code into NIST’s automated pipeline routine and validate functionality of the resulting functionality enhancement.

Task 3: Enhance Existing Metadata Schema for Image Processing

Additional details related to the image data need to be captured for future reference. These include details of how the image data were processed and manipulated, including capturing the parameters and variables associated with the processing operation. Also to be included are details that describe the experiment sufficiently so that a future user of the data can easily identify salient characteristics of the experiment.

These metadata are required for reproducibility, comparison of methods, and reporting. Metadata files shall be created in an automated fashion. These metadata must be unambiguously associated with the original image dataset as well as derived subsets of the data post-processing. Human understandable file names will also be required. A user interface for accessing, viewing, adding to, and manipulating the metadata shall be provided. These metadata shall be compiled in such a way as to be easily extracted and parsed for later analysis. This will involve saving in a JSON or similar format and for later addition to a database.

The Contractor shall:

• Work with BBD cell biologists and data scientists to identify required metadata details and sources from which to pull metadata.

• Develop an extensible schema that can be populated with additional metadata as image data undergo additional processing and analysis steps for adding to metadata files in JSON or another appropriate format approved by NIST.

• Associate metadata files with processed and analyzed image data with a naming scheme and in locations in folders to unambiguously associate metadata with the original image dataset and with derived subsets of the processed image data.

• Provide a user interface for accessing, viewing, adding to, and manipulating the metadata.

Task 4: Reporting

The Contractor shall meet with and provide technical updates to BBD cell biologists and data scientists onsite at least three times per week. The Contractor shall provide monthly progress reports that document the progress, accomplishments, and challenges for the previous month. The reports shall address activities accomplished, deliverables completed, outstanding deliverables, any delays, reasons for delays, plans to mitigate and/or remedy delays, and recommendations that were brought to the attention of the research team and/or NIST Subject Matter Expert (SME).

While specific deliverables for these tasks are articulated below, the nature of Tasks 1 to 3 is such that these tasks will inform one another and, therefore, are in many ways interconnected. Since metadata capture is part of the overall data processing pipeline being enhanced, work on each task may be pursued while other tasks are also being undertaken.

V. PERIOD OF PERFORMANCE

The period of performance shall be 6 months from date of award.

VI. PLACE OF PERFORMANCE

The primary place of performance is the NIST campus in Gaithersburg, MD.

Offsite telework is allowed twice per week and shall incur no additional cost to the Government.

Offsite telework shall be coordinated with the NIST COR and SME prior to execution.

Normal duty hours are M-F 8:30 AM to 5 PM Eastern time except for Federal Holidays.

During closure of the NIST facility due to declared holidays, administrative leave granted to the entire government staff, natural disasters, severe weather, emergencies, staff furloughs, or other closures, the Contractor will not be required to perform services on the campus, unless specifically scheduled. In the event of facility closure the Contractor, if scheduled to work, shall not report to work for the duration of the closure unless directed/approved in writing in advance, or shall arrive/leave as directed in the event of late openings/early closures. In the event of a facility closure, the Contractor will not be compensated nor penalized for the time of the closure.

The Contractor will not be allowed to work at the NIST facility unless a designated government employee is present or unless out-of-hours work is authorized by the Contract Officer (CO) or Contract Officer Representative (COR).

The Contractor will not be allowed to work at the NIST facility during any Federal holidays without prior written approval from the COR and a designated government employee being present.

VII. GOVERNMENT FURNISHED PROPERTY, DATA AND/OR INFORMATION

Any property, data, and/or information provided by the Government during performance remains the property of the Government and shall be surrendered to the Government upon completion or termination of this requirement. Likewise, all deliverables generated hereunder remain the property of the Government.

Government-furnished equipment will be provided in an as-is condition and in a working condition.

The Government will provide the Contractor with all equipment needed to perform tasks 1 to 3.

The Government will furnish the Contractor with an office, desk, chair, computer, monitor, and an office telephone.

NIST will not pay for Wi-Fi or mobile phone charges associated with performance.

The Contractor shall maintain Government furnished supplies, equipment, and work areas in a safe, orderly, and clean condition. The Contractor shall abide by all NIST requirements for physical and logical security of property and equipment. Government furnished supplies and equipment are authorized for official Government business only and may be subject to monitoring at all times.

Items issued will remain the property of the Government and shall not be removed from the NIST campus without a signed property pass. Telephones, copiers, computers, facsimile machines, and other equipment are authorized for official Government business only and shall not be used for personal business.

Space used by the Contractor during performance of services may be used for other purposes during their absences. Items of clothing, personal effects, or equipment cannot be secured by NIST during their absence.

The Government will not incur any liability for theft, damage to, or loss of such personal items.

The Contractor shall conform to facility and systems access security policies, procedures, and controls, consistent with the Federal Government workplace at all places of performance and wear a conspicuous identification badge.

The Contractor shall conform to safety and health policies, procedures, and protocols consistent with the Federal Government workforce.

The Contractor shall comply with the safety policies defined by MML. These safety policies will be outlined in the general NIST safety and Material Measurement Laboratory on-line training courses, which will be made available to the Contractor.

Before work begins the Contractor will be briefed on appropriate NIST/MML safety requirements. This will occur during the first week of the performance period and will be conducted by the SME. After beginning the work at NIST, the contractor will have access to the internal NIST safety website and all the safety policies provided at https://nistgov.sharepoint.com/sites/MML/safety/SitePages/Home.aspx

VIII. TRAVEL

No travel is anticipated at this time. However, if the need for travel is identified, the COR will contact the Contract Officer (CO) directly. If the CO determines that the travel is within scope, a funded modification will be executed bilaterally.

https://nistgov.sharepoint.com/sites/MML/safety/SitePages/Home.aspx

IX. QUALIFICATIONS OF CONTRACTOR KEY PERSONNEL

The Contractor’s assigned key personnel shall meet the following minimum qualifications:

• Minimum 3-year degree in computer science and advanced skills in data analysis, such as machine learning and deep learning

• 4 years of experience with Linux, Windows, and Mac OS operating systems

• 4 years of experience with advanced programming in Python, advanced skills in JSON development, and advanced programming in schema development.

• 2 years of experience creating and using Docker

• 3 years of experience or training in signal and image processing

• 5 years of experience in programming and data organization

• 6 years of experience with NoSQL databases, MongoDB, and source code.

The expectation is that this work will require a full-time (FTE) level of effort (LoE) conducted on a scheduled 8-hour per day basis.

X. DELIVERABLES

Task 1 - Enhance Image Processing Pipeline to Include Application of existing 3D U-Net code

Description Format Quantity Due Date

a. Identify key variables for the 3D model and ensure accessibility of the existing 3D U-Net codebase.

MS Word or PowerPoint document 1 1 month from award

b. Validate code integrity and accuracy of model outputs.

Software functional demonstration 1 2 months from award

c. Ensure comprehensive documentation of code structure for maintainability and future development

Software functional demonstration 1 3 months from award

d. Integrate the 3D U-Net model into the automated pipeline routine and validate end-to-end functionality to ensure accurate operation within the pipeline

Software functional demonstration 1 3 months from award

e. Add code to GitHub GitHub entry of python code and documentation 1 3 months from award

Task 2 - Enhance Image Processing Pipeline with Tracking Routine Integration

f. Identify key variables to be saved at each step of the pipeline and ensure accessibility of the tracking routine codebase.

MS Word or PowerPoint document 1 4 months from award

g. Validate code integrity and accuracy of tracking results.

Software functional demonstration 1 5 months from award

h. Enable track filtering mechanisms within the pipeline and provide user configurable options to modify tracking filters.

Software functional demonstration 1 5 months from award

i. Validate end-to-end functionality to ensure seamless integration and accurate operation of the tracking routine.

Software functional demonstration 1 6 months from award

j. Ensure code accessibility of the image processing pipeline through NIST GitHub repository.

GitHub entry of Python code and documentation 1 6 months from award

Task 3 - Enhance Metadata Schema for Image Processing

k. Enhance metadata schema by collaborating with experimentalists to identify 10 to 15 new metadata terms for collection.

MS Word or PowerPoint document 1 2 months from award

l. Identify and define new image processing steps and associated variables to be saved in the metadata schema

MS Word or PowerPoint document 1 2 months from award

m. Update the metadata schema to incorporate newly identified terms and processing variables.

Software functional demonstration 1 4 months from award

n. Ensure these variables are correctly captured and saved with each processed image.

Software functional demonstration 1 4 months from award

o. Validate metadata collection, consistency, and accessibility within the pipeline.

Software functional demonstration 1 4 months from award

p. Provide a user interface for accessing, viewing, adding to, and manipulating the metadata

Software functional demonstration 1 6 months from award

Task 4 - Reporting

q. Monthly Progress Report MS Word Document and

Updated PowerPoint Presentation

6 10th day of each month of award

XI. INSPECTION AND ACCEPTANCE CRITERIA

As tasks and deliverables are completed, the Contractor shall submit the deliverables for review by the NIST research team/SME. The NIST research team/SME will provide comments on a deliverable within five business days of receipt. The Contractor shall revise and resubmit the deliverable(s) in accordance with the NIST research team’s/SME’s comments and resubmit for NIST research team/SME review and further comment/COR approval. All revisions shall be made at no additional cost to the Government. NIST COR shall be responsible for acceptance of final deliverables.

XII. QUALITY ASSURANCE SURVEILLANCE PLAN

The quality assurance surveillance plan (QASP) is tailored to the work to be performed and provides a basis for the NIST COR to evaluate the quality of the Contractor’s performance. The oversight outlined in this plan will help to ensure that the topics and assessment are maintained at the required levels throughout the period of performance. Further, this plan provides the NIST COR with a proactive way to avoid unacceptable or deficient performance.

Performance Standards:

1. Quality Level – By monitoring the Contractor, the NIST COR will determine whether the Performance Standards outlined in Section XIII. Performance Requirements Summary have been attained.

2. Frequency – During performance, the NIST COR takes periodic measurements (i.e., conduct surveillance), as specific, and will analyze whether the frequency of measurement is appropriate for the work being performed.

3. Management Responsiveness – The NIST COR will determine whether the Contractor has managed the tasks effectively and efficiently with successful completion of the topics and assessment as specified in the Performance Standards set forth in Section XIII.

XIII. PERFORMANCE REQUIREMENTS SUMMARY

Task 1

Required Service Desired Output Performance Standard Monitoring Method

Enhance image processing pipeline to include application of the existing 3D U-Net code

Developed software and MS-Word or PowerPoint Documents

Contractor promptly responds to all government methods of contact and attends scheduled meetings.

Code functions to reliably process and stores images in continuous fashion.

Software management including documentation and versioning is in line with software industry acceptable practices and techniques.

Source code and software test datasets are added to Github.

Deliverable a. submitted no later than the end of the 1st month of the award.

Deliverable b. submitted no later than the end of the 2nd month of the award.

Deliverables c. through e. submitted NLT the 3rd month of the award.

Demonstrations will be attended by, and all outputs and documentation, including GitHub entry will be reviewed and monitored by the NIST SME/research team members to ensure compliance with performance standards.

Task 2

Output Performance Standard Monitoring Method

Enhance image processing pipeline with tracking routine integration

Developed software and MS-Word or PowerPoint Documents

Contractor promptly responds to all government methods of contact and attends scheduled meetings.

Code functions to reliably process and stores images in continuous fashion.

Demonstrations will be attended by, and all outputs and documentation, including GitHub entry will be reviewed and monitored by the NIST SME/research team members to ensure

Software management including documentation and versioning is in line with software industry acceptable practices and techniques.

Source code and software test datasets are added to Github.

Deliverable f. submitted no later than the end of the 4th month of the award.

Deliverables g. through h. submitted NLT the 5th month of the award.

Deliverables h. through j. submitted NLT the 6th month of the award.

Task 3

Output Performance Standard Monitoring Method

Enhance metadata schema for image processing

Developed software and files of metadata embedded into image file, and schema formatted as a MS Word or Excel table or spreadsheet, and user interface

Contractor promptly responds to all government methods of contact and attends scheduled meetings.

A user interface allows viewing and interacting with metadata.

Software management including documentation and versioning is in line with software industry acceptable practices and techniques.

Source code and software test datasets are added to Github.

Deliverables k. to l. submitted no later than the end of the 2nd month of the award.

Deliverables m. to o. submitted no later than the end of the 4th month of the award.

Deliverable p. submitted no later than the end of the 6th month of the award.

Demonstrations will be attended by, and all outputs and documentation, including GitHub entry will be reviewed and monitored by the NIST SME/research team members to ensure

Task 4

Output Performance Standard Monitoring Method

Reporting

MS Word Documents, PowerPoint and/or visual Presentations updated to reflect the progress achieved.

Contractor promptly responds to all government methods of contact and attends scheduled meetings.

Contractor provides written updates of progress, and all visual presentations are updated as appropriate from the previous reports.

Monthly status reports will be reviewed by the NIST SME/COR to ensure

Monthly status reports are submitted NLT the 10th of the month.

XV. GENERAL

The Contractor shall not employ talent for work under this task order if such employee is considered by the COR to be a potential threat to the health, safety, security, general well-being, or operational mission of the installation and/or building and its population.

The Contractor whose actions (e.g., intoxication, debilitation resulting from drug use, insubordination, theft, violation of computer policy or code of conduct) result in any disruption to the workforce may be immediately removed by the CO.

The Contractor shall be responsible for knowing and complying with all site safety regulations. Such regulations include, but are not limited to, general safety, fire prevention, equipment use, material handling, and waste disposal.

The Contractor shall conform to facility and systems access security policies, procedures, and protocols, consistent with the Federal Government workforce at all places of performance.

To gain access to a government facility, the Contractor must be able to obtain a clearance to be issued a Personal Identity Verification (PIV) badge (to be issued by NIST). The Contractor shall immediately report any lost or stolen badge to the COR, his/her designated company representative, and the NIST Security Office.

NIST is a restricted campus. The identification badge is required for access for entry into buildings and is also show to the armed Security Police when entering the campus. The contractor shall wear the visible identification badge provided by the NIST Security Office. The badge must show the full name, title, photo, clearance level, and, if required by NIST the word “Contractor” in front.

The contractor shall turn in the NIST identification badge to the Government security official of the COR at the conclusion of the performance period.

The Contractor shall not respond to any media inquiries. Any inquiries from the media shall be immediately relayed to the COR, NIST SME and/or CO. There shall be no interviews, comments, or any other response without the knowledge and approval of the NIST Public Affairs Office.