Alternatives and similar repositories for notebooks

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

• trasse / OpSeF-IV
  ☆24Updated 5 years ago
• royerlab / cytoself
  Self-supervised models for encoding protein localization patterns from microscopy images
  ☆80Updated 6 months ago
• michaellee1 / CellSeg
  ☆24Updated 2 years ago
• KerenLab / CellSighter
  ☆37Updated 2 years ago
• cytomining / DeepProfiler
  Morphological profiling using deep learning
  ☆123Updated last year
• vanvalenlab / deepcell-label
  Cloud-based data annotation tools for biological images
  ☆84Updated last year
• AllenCell / aics-ml-segmentation
  ☆32Updated 6 months ago
• AllenInstitute / aics-segmentation
  AICS Segmentation (One-Way) Mirror
  ☆45Updated 5 years ago
• AllenInstitute / aics-ml-segmentation
  AICS ML Segmentation (One-Way) Mirror
  ☆27Updated 4 years ago
• cytomining / copairs
  Find profile pairs and compute retrieval metrics between them.
  ☆21Updated last week
• labsyspharm / palom
  Piecewise alignment for layers of mosaics
  ☆35Updated 5 months ago
• NHPatterson / wsireg
  multimodal whole slide image registration in a graph structure
  ☆100Updated last year
• Kapoorlabs-CAPED / VollSeg
  Segmentation method able to detect membrane/nuclei-labelled cells with low signal-to-noise ratio and dense packing in 2D and 3D. Availabl…
  ☆34Updated 3 months ago
• labsyspharm / cylinter
  An Interactive Image Segmentation Filter for Multiplex Microscopy
  ☆31Updated 3 months ago
• CellProfiler / python-bioformats
  Read and write life sciences file formats
  ☆142Updated 7 months ago
• TissUUmaps / TissUUmaps
  TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUma…
  ☆66Updated 2 months ago
• JacobHanimann / scDINO
  Self-Supervised Vision Transformers for multiplexed imaging datasets
  ☆60Updated last year
• uhlmanngroup / splinedist
  SplineDist: Automated Cell Segmentation with Spline Curves
  ☆70Updated last year
• CellProfiling / subcell-embed
  Codebase for training the SubCell models
  ☆18Updated last week
• glencoesoftware / raw2ometiff
  Raw format to OME-TIFF converter
  ☆56Updated 2 weeks ago
• VasylVaskivskyi / microaligner
  Image registration (alignment) software for large microscopy images
  ☆27Updated 2 years ago
• labsyspharm / mcmicro
  Multiple-choice microscopy pipeline
  ☆145Updated last week
• CellProfiler / tutorials
  CellProfiler tutorial pipelines and images
  ☆98Updated last week
• manzt / napari-lazy-openslide
  Lazily load multiscale whole-slide images with openslide and dask
  ☆34Updated 3 years ago
• AllenCell / aics-segmentation
  Part 1 of Allen Cell and Structure Segmenter: classic image segmentation workflow
  ☆25Updated last year
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆39Updated 4 months ago
• ksugar / qupath-extension-cellsparse
  QuPath extension for Cellsparse
  ☆19Updated 9 months ago
• KristinaUlicna / DeepTree
  Jupyter notebooks for deep lineage analysis of single-cell heterogeneity and cell cycling duration heritability.
  ☆30Updated 5 years ago
• CellProfiler / CellProfiler-plugins
  Community-contributed and experimental CellProfiler modules.
  ☆72Updated 3 weeks ago
• jump-cellpainting / 2024_Chandrasekaran_NatureMethods_CPJUMP1
  ☆71Updated 11 months ago