Software

dbittools [github]

A set of tools for working with spatial ‘-omics’ data generated by deterministic barcoding in tissue (DBiT) experiments.

Shoelace Genomics Tools [github]

A python package for RNA sequence data and expression level analysis and utilities for querying the NCBI Gene Expression Omnibus (GEO) database. This package is written for Linux/*nix and uses sratools, bowtie, and RSEM to retrieve FASTQ data, manipulate it, align to reference genomes, and estimate expression levels.

Patch Sorter [github]

Python GUI utility for sorting image patches. Randomly presents user with subregions of an image (“patches”) and lets user select between two categories for each patch, saving the patches as individual *.png files in two output directories.

Brain Histology Segmentation [github]

Some MATLAB functions for segmentation and quantification of lymphocytes, myelin, and collagen in standard histologic brain sections

IHC counting [download ijm]

It is frequently useful to know the proportion of cells staining positively by immunohistochemistry. DAB, a frequently used chromogen, imparts a brown color to tissue that is bound by the primary antibody used. One antigen often probed for is Ki-67, a marker for cells actively diving (i.e. they are outside the G0 phase of the cell cycle). “Ki-67” and “MIB-1” are two different monoclonal antibodies directed against different epitopes of the Ki-67 protein. Often it is helpful to know the proportion of total cells in a tumor that stain positive for either of these markers. This utility, written for ImageJ, automatically counts total nuclei and nuclei with positive staining, and reports the fraction positive, delivering an overlay image of the counted cells in the process.

KerasGAN [github]

Training a Generative Adversarial Network (GAN) using Keras

Spatial Frequency Analysis of IHC [github]

2D FFT tool for analyzing histology images. Originally used for analysis of cytokeratin staining patterns in pituitary adenoma.