SOW_for_RFQ.pdf

Request for Quotation Number 1333ND19QNB640709

Attachment I

BACKGROUND

The Biomaterials Group in the Biosystems and Biomaterials Division (BBD) at the National Institute of

Standards and Technology (NIST), has a nationally and internationally recognized program in biological measurements. NIST’s leadership role involves developing novel measurement protocols, assays and biological reference materials to advance competitiveness in biotechnology and the life sciences.

An important component of the NIST mission is, whenever possible, to develop measurements with versatile, transparent and transferrable methods. A commercially available, automated, inverted fluorescence microscope with an open development environment is needed to advance that program by enabling the development of platform agnostic code to operate the microscope that is transferable to NIST stakeholders’ microscopes.

In addition, because of the small size of many biological features, structured illumination capability is crucial to obtain image resolution higher than the diffraction limit, which would particularly benefit the biomanufacturing, microbiome, precision medicine and synthetic biology programs.

REQUIRED SPECIFICATIONS

1. The inverted, automated research grade microscope shall have an eyepiece for visual observation, dual camera ports, motorized filter turret, motorized condenser and motorized, 6 position nosepiece for objectives and tilting condenser arm.

2. All microscope functions shall be controlled via hardware, whether touch-screen pad, programmable joystick buttons or easy to access controls on the microscope body, and through the software. Software shall control and query multiple microscope and camera functions. At a minimum, image acquisition, processing, visualization and hardware status must be functions of the software.

3. The microscope shall have the optomechanics to perform fluorescence, brightfield, phase contrast and differential interference contrast (DIC) imaging.

4. The microscope shall have structured illumination hardware integrated or be upgradable to structured illumination.

5. Motorized nosepiece rotation must be controlled by controls on microscope body or touch pad or programmable joystick shortcuts and/or software icons.

6. Shall have image based autofocus.

7. Shall be able collect z stacks of a minimum of 50 images.

8. Shall be able to automatically combine multiple images into a single focused 2D image, also called extended depth of field or extended focus.

9. One objective of each type must be provided:

a. 4x or 5x Flatfield Fluorite, NA in the range of 0.13 to 0.16, PH for plastic vessels

b. 10x: Flatfield Fluorite, NA in the range of 0.3 to 0.45 PH for plastic vessels

c. 40x oil immersion: Flatfield Fluorite, 1.30NA, DIC

d. 60x or 63x oil immersion: Flatfield Apochromat, 1.40NA, DIC

e. 60x or 63x water immersion: (non-flatfield acceptable), Apochromat, NA in the range of 1.15 to 1.2.

10. Shall have a 6 position motorized fluorescence filter turret with following high performance or high efficiency filter sets. These types of filters are manufactured to provide passband transmission, maximize out of band blocking and extremely steep slopes from rejection to transmission regions. One filter cubes for each of the following fluorophores must be provided:

a. DAPI

b. GFP/FITC

c. DSRed/TRITC/Cy3

d. TexasRed/mRFP

11. Shall have Large chip, ultra sensitive high dynamic range sCMOS camera: Hamamatsu ORCA Flash4.0 or similar, as determined by NIST technical expert. Minimum sensor dimensions: 13 mm x 13 mm. 2048x2048 pixels in array. Minimum quantum efficiency of 80% from 500 to 600 nm and 55% at 750 nm. Minimum full resolution frame rate: 30 frames per second. Minimum Dynamic Range 30,000:1, 16-bit digital output.

Minimum: 0.75e- median read noise.

12. Microscope must be fitted with a transmitted Light LED, controllable through microscope hardware and software.

13. Microscope must have a software controlled solid state LED fluorescence source equipped with a light guide to the microscope port. The first peak of the light source shall be in the range of 355 to 395 nm and must be continuous to a second peak in the near infrared in the range from 720 to 770 nm.

14. Microscope shall have an x,y motorized stage with encoder, a minimum XY travel distance of 110 mm x 70

mm. Universal stage or stage insert(s) to hold well plates, petri dishes and slides.

15. Microscope shall have fully automated software to control microscope, acquire and analyze images, save and recall user-defined imaging methods. Imaging capabilities: x,y slice, z stack, wavelength, time lapse, multi-point, image tiling. Image stitching with adjustable stitching settings. Create sequence of acquisition tasks within software with the ability to have conditional workflows. Ability to designate regions of interest and image only within those regions. Automated multi-dimensional acquisition for imaging of -6, -12, -24, -48 and -

96 well plates and ability to define custom regions within individual wells.

16. Minimum image processing, analysis and visualization capabilities shall be: Automated (Length, area, long and short axes) and manual (length, area, angles, counts, long and short axes, 3D length) image measurement of image object shape using freehand drawing or preset morphological features, and intensity measurement.

Image segmentation. Automated object count. Capability to do erosion, dilation, opening and closing on entire image or ROI. Ability to do statistics on measurements. Save and recall data and image analysis workflows. 2D and 3D deconvolution. Ability to visualize z stack data in a user-define volume and as slices along each axis.

17. Must have integrated, trainable, machine learning software for batch image segmentation for large, multidimensional (x,y,z, t, phase or DIC, fluorescence) 2D and 3D datasets. (In this context, “trainable” means that sample image data can be input into the machine learning algorithm that uses that data to process the remainder of the dataset.) Segmentation trained on the first image will be used to process the remainder of the dataset.

18. Manufacturers software must contain an open development environment for incorporating code for customized microscope acquisition and image analysis using a non-proprietary language such as Python or Javascript.

External applications commonly used for image acquisition and processing such as Matlab and ImageJ must be able to be integrated into workflow. Results from external applications can be transferred back into microscope software for further use.

19. Minimum requirements for workstation: Hewlett Packard Z6 or similar with 2, 4 TB hard drives and 8 GB graphical processing unit (GPU).

20. Minimum requirements for workstation monitor: 27” Backlight LED monitor.

21. The microscope system, including all hardware and microscope control and data acquisition software, shall be assembled and serviced by technicians who are trained and authorized by the microscope manufacturer. Service for the microscope must be arranged through direct contact with the microscope manufacturer, not a third party.

INSTALLATION AND TRAINING

The Contractor shall install the inverted, automated fluorescence microscope at the NIST Gaithersburg, MD campus. Installation shall include, at a minimum, uncrating/unpackaging of all equipment, set-up and hook-up of all equipment, start-up, demonstration of specifications, and removal of all trash.

The Contractor shall schedule and facilitate training for three (3) NIST personnel, on-site at NIST Gaithersburg.

The training shall provide a thorough demonstration of all equipment functions, equipment operation and basic troubleshooting. The training may be completed on-site at NIST immediately after installation and demonstration of specifications.

WARRANTY

The Contractor shall provide, at a minimum, a one year warranty for the equipment. The warranty shall cover all parts, labor and travel. The warranty shall commence upon successful completion of delivery, installation, training and demonstration of all required specifications.

ACCEPTANCE

Acceptance will occur after the NIST Technical Point of Contact has confirmed that the microscope meets all specifications of this statement of work. Should any deficiencies be noted prior to final acceptance, the

Contractor will be notified and provided the opportunity to correct all deficiencies at their expense, in accordance with the commercial terms and conditions of the contract.

PERIOD OF PERFORMANCE

Delivery, installation and training shall be completed not later than 90 days after award.

PLACE OF PERFORMANCE

Installation and training shall be performed at the National Institute of Standards and Technology, 100 Bureau

Drive, Gaithersburg, MD 20899-8543.