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    78 repositories

    • JUMP-single-cell

      Public
      Single cell analysis of the JUMP Cell Painting consortium pilot data (cpg0000)
      pythonimage-processingcellprofilerimage-analysiscell-paintingpycytominer
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •5•4•2•0•Updated Mar 6, 2025Mar 6, 2025

    • pediatric_cancer_atlas_analysis

      Public
      Image2Image Translation Model Optimization and Training to Predict Stains from Brightfield with Cell Painting Data
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated Mar 6, 2025Mar 6, 2025

    • waysciencelab.com

      Public
      Homepage for all happenings in the Way Lab at CU Anschutz
      data-sciencemachine-learningbiologyhealth
      SCSS
      •
      BSD 3-Clause "New" or "Revised" License
      •9•4•2•0•Updated Mar 4, 2025Mar 4, 2025

    • coSMicQC

      Public
      Single cell Morphology Quality Control (coSMicQC)
      quality-controlimage-based-profilingmicroscopy-image-analysis
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•7•18•1•Updated Mar 3, 2025Mar 3, 2025

    • pediatric_cancer_atlas_profiling

      Public
      Image analysis and image-based profiling of pediatic cancer cell lines to extract morphological profiles.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •3•1•1•1•Updated Mar 3, 2025Mar 3, 2025

    • pyroptosis_signature_data_analysis

      Public
      Analysis repository for the pyroptosis morphology map
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•15•1•Updated Feb 27, 2025Feb 27, 2025

    • sc-tracking-optimization

      Public
      This repo aims to track cells in the best way possible
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Feb 25, 2025Feb 25, 2025

    • gene_dependency_representations

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •5•2•0•0•Updated Feb 24, 2025Feb 24, 2025

    • pyroptosis_live-cell_timelapse

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•1•Updated Feb 22, 2025Feb 22, 2025

    • CFReT-screen-mAP-analysis

      Public
      Analysis notebooks applying mean average Precision (mAP) to the CFReT screen image-based profiles dataset.
      Jupyter Notebook
      •1•0•3•0•Updated Feb 19, 2025Feb 19, 2025

    • CytoDataFrame

      Public
      An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•14•0•Updated Feb 18, 2025Feb 18, 2025

    • virtual_stain_flow

      Public
      For developing virtual staining models
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated Feb 14, 2025Feb 14, 2025

    • nViz

      Public
      A tool for creating and visualizing n-dimensional microscopy images.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•16•3•Updated Feb 14, 2025Feb 14, 2025

    • nuclear_speckles_analysis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•0•Updated Feb 7, 2025Feb 7, 2025

    • playbooks

      Public
      Playbooks relevant to the operations of the Way Lab and similar labs.
      Creative Commons Zero v1.0 Universal
      •1•0•3•0•Updated Feb 7, 2025Feb 7, 2025

    • nf1_schwann_cell_morphology_signature

      Public
      This repository contains all the modules to split and train a binary classification model to predict NF1 null and wildtype genotype.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •2•0•1•2•Updated Feb 5, 2025Feb 5, 2025

    • gc-saguaro_udm_bucket

      Public
      Cloud Storage bucket on Google Cloud for Saguaro and UdeM data transfer.
      cloudresourcebucket
      CUE
      •1•0•0•0•Updated Feb 4, 2025Feb 4, 2025

    • nf1_schwann_cell_painting_data

      Public
      This repository contains all the modules to perform image-based analysis with CellProfiler on NF1 Schwann cell data.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •6•5•6•1•Updated Jan 31, 2025Jan 31, 2025

    • demo-uca-isilon-python

      Public
      Demonstrating capabilities with the University of Colorado Anschutz (UCA) Isilon storage solution using Python.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•3•0•Updated Jan 25, 2025Jan 25, 2025

    • NF1_3D_organoid_profiling_pipeline

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•7•4•Updated Jan 25, 2025Jan 25, 2025

    • live_cell_timelapse_apoptosis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•5•0•Updated Jan 19, 2025Jan 19, 2025

    • CPBS7601

      Public
      Course on computing skills in biomedical informatics
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •9•0•0•1•Updated Jan 14, 2025Jan 14, 2025

    • gc-bucket-alsf-predicting-nuclear-speckles

      Public archive
      GCP bucket for ALSF collaborations on predicting nuclear speckles. (now archived outside of these cloud resources)
      cloud-resourcesbucket
      HCL
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated Jan 14, 2025Jan 14, 2025

    • targeted_fibrosis_drug_screen

      Public
      Image analysis and image-based profiling of a fibrosis drug screen to identify compound hits using a machine learning model.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •2•2•1•0•Updated Jan 8, 2025Jan 8, 2025

    • predicting-cell-injury-compounds

      Public
      Processing cell-injury profiles using Pycytominer to generate selected features profiles for training a multi-class regression model to identify cellular injury.
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •2•1•0•0•Updated Dec 24, 2024Dec 24, 2024

    • pairwise_compare

      Public
      Python
      •
      Creative Commons Attribution 4.0 International
      •0•1•3•1•Updated Dec 13, 2024Dec 13, 2024

    • Phenotypic_severity_and_variance

      Public
      Quantifying Zebrafish opercle bone morphology
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•1•0•Updated Dec 6, 2024Dec 6, 2024

    • GFF_2D_organoid_prototyping

      Public
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Nov 11, 2024Nov 11, 2024

    • sandbox

      Public
      A place to mess around learning github
      MIT License
      •23•0•0•2•Updated Nov 6, 2024Nov 6, 2024

    • demo-cellprofiler

      Public
      Demonstrating various CellProfiler development or implementations.
      Shell
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•0•Updated Oct 23, 2024Oct 23, 2024