Alternatives and similar repositories for notebooks:

Users that are interested in notebooks are comparing it to the libraries listed below

• KerenLab / CellSighter
  ☆31Updated last year
• angelolab / ark-analysis
  Integrated pipeline for multiplexed image analysis
  ☆84Updated this week
• labsyspharm / cylinter
  An Interactive Image Segmentation Filter for Multiplex Microscopy
  ☆28Updated last month
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆36Updated last year
• michaellee1 / CellSeg
  ☆22Updated last year
• TissUUmaps / TissUUmaps
  TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUma…
  ☆51Updated last month
• jump-cellpainting / 2024_Chandrasekaran_NatureMethods
  ☆60Updated last month
• royerlab / cytoself
  Self-supervised models for encoding protein localization patterns from microscopy images
  ☆75Updated 6 months ago
• carpenterlab / 2016_Bray_NatureProtocols
  Supporting data files, documentation, and updated tips for the Cell Painting protocol
  ☆21Updated 3 years ago
• vanvalenlab / deepcell-label
  Cloud-based data annotation tools for biological images
  ☆78Updated last year
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆86Updated last month
• labsyspharm / palom
  Piecewise alignment for layers of mosaics
  ☆23Updated 3 months ago
• AllenInstitute / aics-segmentation
  AICS Segmentation (One-Way) Mirror
  ☆45Updated 4 years ago
• labsyspharm / mcmicro
  Multiple-choice microscopy pipeline
  ☆124Updated 2 weeks ago
• mehta-lab / dynamorph
  Learn morphological states of dynamic cells
  ☆12Updated last year
• cytomining / cytominer
  Methods for Image-Based Cell Profiling
  ☆50Updated 10 months ago
• JacobHanimann / scDINO
  Self-Supervised Vision Transformers for multiplexed imaging datasets
  ☆49Updated 8 months ago
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆52Updated 9 months ago
• BodenmillerGroup / steinbock
  A toolkit for processing multiplexed tissue images
  ☆59Updated 2 weeks ago
• uhlmanngroup / splinedist
  SplineDist: Automated Cell Segmentation with Spline Curves
  ☆67Updated 5 months ago
• broadinstitute / cell-health
  Predicting Cell Health with Morphological Profiles
  ☆36Updated 3 years ago
• mahmoodlab / MAPS
  Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications
  ☆50Updated last year
• AllenCell / aics-segmentation
  Part 1 of Allen Cell and Structure Segmenter: classic image segmentation workflow
  ☆28Updated 8 months ago
• glencoesoftware / raw2ometiff
  Raw format to OME-TIFF converter
  ☆50Updated 2 weeks ago
• CellProfiler / CellProfiler-plugins
  Community-contributed and experimental CellProfiler modules.
  ☆63Updated last month
• AllenCell / aics-ml-segmentation
  ☆31Updated 2 years ago
• CellProfiler / tutorials
  CellProfiler tutorial pipelines and images
  ☆93Updated this week
• carpenter-singh-lab / 2023_Cimini_NatureProtocols
  Optimizing the Cell Painting assay for image-based profiling
  ☆19Updated 2 months ago
• fish-quant / big-fish
  Toolbox for the analysis of smFISH images.
  ☆59Updated last year