astropathjhu Goto Github PK
Name: AstroPath
Type: Organization
Bio: AstroPath Platform Code
Location: Baltimore
Name: AstroPath
Type: Organization
Bio: AstroPath Platform Code
Location: Baltimore
The AstroPath Pipeline was developed to process whole slide multiplex immunofluorescence data from microscope to database at single cell resolution.
Action for checking out a repo
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.
Python Deep Zoom Tools
MaSS (Merge a Single Sample); code to merge multipass inForm data
Multiplex Immunoflouresence Titration Optimization (mIFTO) R Package
Python libraries for SciScript, Jupyter Notebooks
R libraries for SciScript, Jupyter Notebooks
Create a segmentation tool for comparing inform and ML approaches while creating an unbiased ground truth
Perform multi-modality whole slide to whole slide pathology image registration
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