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astropathpipeline

The AstroPath Pipeline was developed to process whole slide multiplex immunofluorescence data from microscope to database at single cell resolution.

checkout

Action for checking out a repo

convertim3

The executable was written by Richard Wilton to extract the bitmap and metadata information from the akoya im3 image files.ConvertIm3Path is a powershell code, added by Benjamin Green and is a soft wrapper for the executable to run on the sample level and is dependent on the images being in the AstropathPipeline directory format. ConvertIm3Cohort.ps1 is a wrapper for ConvertIm3Path.ps1 which runs through all specimens in a directory, the cohort is hard coded at present and should be modified in the code.

deepzoom.py

Python Deep Zoom Tools

mass

MaSS (Merge a Single Sample); code to merge multipass inForm data

mifto

Multiplex Immunoflouresence Titration Optimization (mIFTO) R Package

rocpicker

sciscript-python

Python libraries for SciScript, Jupyter Notebooks

sciserverr

R libraries for SciScript, Jupyter Notebooks

segtool

Create a segmentation tool for comparing inform and ML approaches while creating an unbiased ground truth

wsimir

Perform multi-modality whole slide to whole slide pathology image registration