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mifqc Public
Quality Control statistics for Mulitplex ImmunoFluorescence Images: (1) Entire Image, (2) Image Tiles, and (3) Cell Tables.
Python UpdatedSep 4, 2025 -
astir Public
Forked from camlab-bioml/astirastir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
Python GNU General Public License v2.0 UpdatedJun 25, 2025 -
cio-wsi-segmentation Public
Forked from jason-weirather/cio-wsi-segmentationRun whole slide segmentation
Python Other UpdatedJun 23, 2025 -
good-neighbors Public
Forked from jason-weirather/good-neighborsIdentify neighborhoods based on local cell populations.
Jupyter Notebook Apache License 2.0 UpdatedJun 14, 2025 -
seg-flow Public
Forked from jason-weirather/seg-flowWorkflow manager for running segmentation on tiles and recombining them.
Python Apache License 2.0 UpdatedNov 6, 2024 -
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deepcell-toolbox Public
Forked from jason-weirather/deepcell-toolboxData processing tools associated with deepcell
Python Other UpdatedOct 23, 2024 -
deepcell-tf Public
Forked from jason-weirather/deepcell-tfDeep Learning Library for Single Cell Analysis
Python Other UpdatedOct 23, 2024 -
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bioformats2raw Public
Forked from glencoesoftware/bioformats2rawBio-Formats image file format to raw format converter
Java GNU General Public License v2.0 UpdatedOct 7, 2024 -
ome-slicer Public
Forked from jason-weirather/ome-slicerPerform basic operations like crop on OME tiff files and preserve structure
Python Apache License 2.0 UpdatedOct 3, 2024 -
tiff-inspector Public
Forked from jason-weirather/tiff-inspectorA package for examining the structure and contents of the metadata contained within tiff files
Python MIT License UpdatedOct 2, 2024 -
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raw2ometiff Public
Forked from glencoesoftware/raw2ometiffRaw format to OME-TIFF converter
Java GNU General Public License v2.0 UpdatedJul 12, 2024 -
SamplerBox Public
Forked from josephernest/SamplerBoxSamplerBox is a sampler musical instrument based on RaspberryPi.
Python UpdatedMay 9, 2024 -
CELESTA Public
Forked from plevritis-lab/CELESTAAutomate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information for multiplexed in situ imaging data. No training dataset wi…
R Apache License 2.0 UpdatedMay 7, 2024 -
ome_convert_deid Public
Convert from qptiff (and scn?) to ome tiff and remove some metadata.
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OT-scOmics Public
Forked from cantinilab/OT-scOmicsThis Python package will allow you to replicate the experiments from our research on applying Optimal Transport as a similarity metric in between single-cell omics data.
Python GNU General Public License v3.0 UpdatedFeb 3, 2023 -
fgsea_plotupdown Public
A modified version of plotEnrichment() from FGSEA. This version takes in two pathways instead of one: an UP and a DOWN -regulated pathway. Both are plotted on the same enrichment plot.
R MIT License UpdatedAug 23, 2021 -
SCSeqFxs Public
Some functions for streamlined single cell sequencing analysis.
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genelowercase Public
Forked from iddryg2/genelowercaseA script to convert every gene name to capitalized first letter, every other letter lowercase. This is to convert a gene set for GSEA. https://www.gsea-msigdb.org/gsea/index.jsp March 2021 - Ian Dryg
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PixelDistance Public
Forked from iddryg2/PixelDistanceUsing multi-channel microscopy images, calculates the minimum distance between two markers. In this case, it was used to calculate how invasive tumor cells were in lymph nodes by measuring the mini…
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inform-verify Public
Forked from jason-weirather/inform-verifyVerify InForm format assumptions
Python Apache License 2.0 UpdatedMar 13, 2019 -
Vertex Component Analysis in Python
Python Apache License 2.0 UpdatedJun 12, 2018
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