6515--Halo Software for Analysis

1901 Veterans Memorial Dr.

STATEMENT OF WORK (SOW)

A. GENERAL INFORMATION

Title of Project: Purchase of Software for Quantitative Tissue Analysis of Histological Slides.

Scope of Work: The Research Department located at the Central Texas Veterans Health Care System (CTVHCS), 1901 S. 1st Street, Temple, Texas has requested to purchase a software package that will allow for quantitative tissue analysis of immunohistochemical and fluorescently stained slides. This software will be used as shared software for basic science research.

Background: Many of the basic science investigators at CTVHCS perform image analyses in different tissues. In order to improve the speed and consistency of manual image analyses, software can be used to improve workflow. The desired software needs to be a platform that is able to perform quantitative tissue analysis in digital pathology, that allows for robust and consistent pathological analyses to be performed. The requested software platform also needs to be flexible and allow Research Service to choose the specific modules containing the algorithms needed for by investigators. The use of this software will increase the capability of researchers and increase the speed and quality of analyses resulting in improved research output.

DESCRIPTION of SOFTWARE: This is a request for software that will provide quantitative tissue analysis of digitally scanned histology slides. Below are the requirements for the software:

The software must be modular with regard to number of workstations and various types of analytical algorithms.

Area quantification of fluorescent slides in base module: The base software must be able to perform area quantification for an unlimited number of fluorescent dyes. The software should be able to quantify and report dye positive areas, average intensity for each dye, binned positivity based on intensity (0, 1+, 2+ and 3+) and areas of colocalization when multiple dyes are analyzed.

Area Quantification immunohistochemistry (IHC) in base module: The base IHC software must be able to quantify up to five brightfield stains on a per area. This function needs to be able to quantify and reports stain positive area, average stain optical density for each stain, binned positivity based on optical density (0, 1+, 2+ and 3+), and area of colocalization (when multiple stains are analyzed).

Optional modules: In addition to the standard base software (area quantification of fluorescence and IHC slides), as per software license, the CTVHCS Research Service has the opportunity to choose three additional modules, based on needs of investigators, out of the ones described below:

The software must have optional modules able to perform single and multiplexed brightfield and fluorescent quantification for up 5 stains in any cellular compartment (e.g. nucleus, cytoplasm, membrane) and output user-defined cell phenotypes based on stain positivity on a per cell basis.

The software must have optional modules able to report morphological and multiplexed expression data on a cell-by-cell basis across entire tissue sections and able to maintain an interactive link between cell data and cell image.

The software must have optional modules that will allow sorting and filtering capabilities that allow users to mine millions of cells while visually assessing corresponding cell populations. For example, cells can be sorted according to a biomarker intensity and be able to immediately locate cells with highest intensity in the image.

The software must have optional module that is able to report morphological and multiplexed expression data for tissue sections and individual cells.

The software must have optional oncology modules that can perform immune cell quantification, serial section and stain analysis, tissue microarray segmentation.

The software must have optional neuro/muscular and vascular modules that can perform axon quantification, microglial quantification, branch structure for vessels, muscle fiber quantification.

The software must have optional metabolism modules that can perform islet quantification for either IHC or fluorescence and vacuole quantification.

The software must have optional spatial analysis modules that can perform nearest neighbor analysis, infiltration analysis and proximity analysis

The software must be compatible with a broad spectrum of image and digital slide formats that include Leica (SCN, LIF), Olympus (VSI), Zeiss (CZI), Nikon (ND2), as well as standard non-proprietary (e.g. JPG, TIF).

The software needs to be able to use parallel processing technology to perform analysis of images.

The software must be able to scale from a standard 4 core CPU to a dual processor Xenon system to perform mathematical analysis.

Free access to an online learning library with videos and other training items to help end users.

SHIPPING: The software will be provided with a unique key allowing for downloading of their software. Indica Labs personnel will perform the initial installation.

Training: Purchase of the software includes an initial on-site training that will last approximately 2 hours. After this, vendor personnel will provide off-site remote training as needed for the first year after purchase.

SERVICE and WARRANTY: Perpetual license and access to 3 modules. Full software support including remote training provided during the first year.