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    73 repositories

    • 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

    • 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•1•Updated Jan 14, 2025Jan 14, 2025

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

      Public
      GCP bucket for ALSF collaborations on predicting nuclear speckles.
      cloud-resourcesbucket
      HCL
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated Jan 14, 2025Jan 14, 2025

    • 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•1•0•Updated Jan 14, 2025Jan 14, 2025

    • GFF_3D_organoid_profiling_pipeline

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•5•3•Updated Jan 14, 2025Jan 14, 2025

    • coSMicQC

      Public
      Single cell Morphology Quality Control (coSMicQC)
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•7•18•0•Updated Jan 14, 2025Jan 14, 2025

    • pyroptosis_signature_data_analysis

      Public
      Analysis repository for the pyroptosis morphology map
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•15•0•Updated Jan 13, 2025Jan 13, 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•4•1•Updated Jan 13, 2025Jan 13, 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
      •1•1•12•0•Updated Jan 13, 2025Jan 13, 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•2•Updated Jan 8, 2025Jan 8, 2025

    • live_cell_timelapse_apoptosis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•5•1•Updated Jan 8, 2025Jan 8, 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

    • gene_dependency_representations

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •5•2•0•0•Updated Jan 6, 2025Jan 6, 2025

    • pyroptosis_live-cell_timelapse

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•4•Updated Jan 4, 2025Jan 4, 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•0•0•0•Updated Dec 24, 2024Dec 24, 2024

    • 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 Dec 20, 2024Dec 20, 2024

    • nuclear_speckles_analysis

      Public
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •1•0•1•1•Updated Dec 14, 2024Dec 14, 2024

    • pairwise_compare

      Public
      Python
      •
      Creative Commons Attribution 4.0 International
      •0•1•2•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

    • gc-saguaro_udm_bucket

      Public
      Cloud Storage bucket on Google Cloud for Saguaro and UdeM data transfer.
      cloudresourcebucket
      1•0•0•1•Updated Dec 2, 2024Dec 2, 2024

    • 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•0•1•Updated Nov 27, 2024Nov 27, 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
      •22•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

    • CFReT-compound-prioritization-analysis

      Public
      Jupyter Notebook
      •1•1•0•0•Updated Oct 22, 2024Oct 22, 2024

    • CP_Parallel

      Public
      Traditionally, headless mode for CellProfiler can only run with one worker at a time with one set of images, which can take a long time sequentially. CP Parallel will run multiple instances of CellProfiler in parallel across plates.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•7•0•Updated Sep 23, 2024Sep 23, 2024

    • playbooks

      Public
      Playbooks relevant to the operations of the Way Lab and similar labs.
      Creative Commons Zero v1.0 Universal
      •1•0•1•0•Updated Sep 16, 2024Sep 16, 2024

    • phenotypic_profiling

      Public
      Machine learning for predicting 15 single-cell phenotypes from cell morphology profiles
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •3•2•0•0•Updated Sep 16, 2024Sep 16, 2024

    • NIH_Where2Submit

      Public
      This is a tool to help you figure out where to submit your grant in the NIH
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•3•0•Updated Sep 9, 2024Sep 9, 2024

    • Kan_we_predict_phenotypes

      Public
      A repo testing KANs on Image-based profiles
      Jupyter Notebook
      •2•0•1•0•Updated Sep 2, 2024Sep 2, 2024