Breast Cell Types: GSEA Pathway Analyzer

Analytic tool for dissecting the biological processes in each breast cell type, across every possible pairwise comparison of cell types

Breast Cell Atlas: Transcript Finder (R/Shiny App)

Supplementary Web Application: A cellular and transcriptomic dissection of the human breast for studying mechanisms of cell and tissue function (2022)

A high-throughput imaging and quantification pipeline for the EVOS imaging platform.

Self-contained imaging systems are versatile instruments that are becoming a staple in cell culture laboratories. Many of these machines possess motorized stages and on-stage incubators that permit programmable imaging of live cells that make them a sensible tool for high-throughput applications. The EVOS imaging system is such a device and is capable of scanning multi-well dishes and stitching together multiple adjacent fields to produce coherent individual images of each well. Automated batch analysis and quantification of these tiled images does however require off-loading files to other software platforms. Our initial attempts to quantify tiled images captured on an EVOS device was plagued by some expected-and other unforeseeable-issues that arose at nearly every stage of analysis. These included: high background, illumination and stitching artifacts, low contrast, noise, focus inconsistencies, and image distortion-all of which negatively impacted processing efficiency. We have since overcome these obstacles and have created a rigorous cell counting pipeline for analyzing images captured by the EVOS scan function. We present development and optimization of this automated pipeline and submit it as an effective and facile tool for accurately counting cells from tiled images