Specifications.pdf

Statement of Work (SOW) Project: Fluorescence Microscope Purchase

GENERAL INFORMATION

1.0 Scope of Work: The UDSA-ARS is requesting bids for purchase of a new Fluorescence

Microscope Specifications for the purchase are itemized below.

2.0 Background: The USDA-ARS-DFRC uses this microscope to visualize genes and morphology of rumen and microbial samples. This work will allow us to verify key populations and tissues involved in the reduction of methane emissions. This equipment could also be used to identify gene expression in plants as well as mammalian tissues.

CONTRACTOR REQUIREMENTS

3.0 Technical Requirements/Tasks:

Most fluorescence microscopes require a dedicated room to ensure darkness while visualizing, with the space constraints at the USDA-DFRC, we will need a microscope that has an enclosed fluorescence component. The microscope will need to have 3 filters to visualize DAPI, FITC, and TexasRed. It will have to allow modifications/additions of filters if more colors are needed in the future. It will need to have the capabilities to do phase and also light microscopy to be useful for daily use. The microscope will also need to have a variety of objectives (4x, 10x, 40x, 100x) so that the magnification can be adjusted for different cell and tissue samples.

The microscope will need to have software that will allow for calculating the number of protozoa and cells which will act as a time saver over our current methods.

Brand name or equal:

Keyence Fluorescent Microscope

Equipment must include:

• Fluorescent microscope o Excluding the computer and monitor, the installation space of the microscope unit plus lighting source must be within 500 mm (H) x 465 mm (W) x 500 mm (D) when the panel is closed o Must be self contained o Must be able to visualize slides, and multi-well plates o The microscope must include, as standard components, an electronic shutter, XY and Z motorized stages, an electronic revolver (to hold 6 objectives from 2x- 100x, must be compatible with both Plan Fluor and Plan Apochromat lenses), an electronic filter turret (to hold 4 filters), electronic color camera filter, electronic phase-contrast slit switching mechanism, electronic dimmer filters, and an electronic aperture control; it is necessary that all of these components can be operated with the mouse.

o Must have DAPI, FITC, and TexasRed filters o Must be able to perform phase contrast, bright field microscopy as well as fluorescence microscopy o The product must have a built-in vibration dampening system with the ability to use up to 100x objectives in a typical lab environment o The microscope must be able to recall all capture settings which include the shutter, aperture, light intensity, XYZ stage position, magnification, filter, imaging mode (brightfield/fluorescence/phase). In addition, there must be Zero manual/mechanical adjustments related to the microscope structure or light path (aperture, focus, stage, condenser, lighting).

Everything must be only controlled electronically.

o The microscope must be equipped with a 14 bit monochrome CCD that is cooled to a temperature that is lower than the ambient temperature by at least 25°C. The camera also needs to have the capability to image into the near infrared spectrum (800-900nm range). The microscope must also be furnished with a mechanism that can capture full-color images using color filters inserted under electronic control.

o The microscope must be equipped a “low photobleach mode” which physically blocks the light to the sample when it is just stationary. Light is only let through when we move the sample or change the capture settings.

o The number of pixels that can be recorded in a single image (not stitched) must be at least 4080 x 3060 o Must have software to assist with counting protozoa and cells o The analysis software must include some basic image processing software such as Haze reduction (no-neighbor deconvolution), image overlays, scale bar, cut/paste, zoom, lookup table, black balance.

o The microscope must include a function to record a video at a frame rate of 95 fps or higher o The microscope must be able to do time lapse imaging with different capture conditions include different locations of interest, exposure time, focus, z Stack, lens magnifications, and filters o The microscope must include a software which can track multiple targets moving over time. Tracking can be using their brightness or hue/color and data output includes XY position, speed, brightness and also include a data plot o The microscope must include a function that automatically selects cells based on the contour, color contrast, etc. and automatically counts/calculates the number of cells, area, perimeter, Feret diameter, major axis, minor axis, and/or integrated brightness value. This software must be compatible with brightfield, phase and fluorescence imaging. The microscope must also include a function that, using selected image information as a target area, allows the user to set conditions again for images in each of such target areas and automatically counts various items. This function must also enable the user to measure area ratios or the like easily o Optical sectioning image mode must be available. Optical sectioning’s operating principal is a Structured Illumination Microscopy (SIM) based design with a built in spatial light modulator using a programmable liquid filter (LC filter), projecting structured light patterns that can be adjusted to accommodate a variety of samples, vessel types and fluorescence intensities. The built-in software will utilize a user defined structured projection and raster the light pattern across each focal plane to be captured. The software then utilizes an algorithm to perform a scaled subtraction of out of focus fluorescence light, isolating in-focused fluorescence signal which will allow construction of high-resolution 3D models. Both 1D slits and 2D pinhole options must be available for maximum flexibility o The microscope must include an image cytometer function that can count/aggregate cells, areas, etc. for each well in a well plate. It is necessary to display statistics from acquired data with a heat map or histogram for each well or field of view. It must be possible to conduct analysis on multiple well plates under the same condition in a batch. It must be possible to save images that were the analysis base as a stitched image without reducing the resolution

• Training o This is a very sensitive bit of equipment and therefore it is imperative that at least one individual at DFRC receives training on the microscope to keep it in good working order

4.0 Government Furnished: NA

5.0 Deliverables / Schedule: Delivery within 90 days of order

6.0 Travel: NA

7.0 Contractor’s Key Personnel: Not identified

8.0 Security Requirements: Vendor is not required for installation

9.0 Data Rights: Not applicable

10.0 Section 508 – Electronic and Information Technology Standards: Not applicable