Alternatives and similar repositories for notebooks:

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

• carpenterlab / 2016_Bray_NatureProtocols
  Supporting data files, documentation, and updated tips for the Cell Painting protocol
  ☆19Updated 3 years ago
• mehta-lab / dynamorph
  Learn morphological states of dynamic cells
  ☆12Updated last year
• labsyspharm / cylinter
  An Interactive Image Segmentation Filter for Multiplex Microscopy
  ☆28Updated 2 months ago
• royerlab / cytoself
  Self-supervised models for encoding protein localization patterns from microscopy images
  ☆75Updated 4 months ago
• broadinstitute / cell-health
  Predicting Cell Health with Morphological Profiles
  ☆35Updated 2 years ago
• CellProfiler / CellProfiler-plugins
  Community-contributed and experimental CellProfiler modules.
  ☆61Updated last week
• AllenCell / aics-ml-segmentation
  ☆30Updated 2 years ago
• cytomining / cytominer
  Methods for Image-Based Cell Profiling
  ☆49Updated 8 months ago
• GuignardLab / napari-sc3D-viewer
  A plugin to visualise 3D spatial single cell omics
  ☆21Updated 9 months ago
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆34Updated last year
• lowe-lab-ucl / arboretum
  Track and lineage visualization with btrack and Napari
  ☆44Updated 2 months ago
• psteinb / b3get
  a python module to download Broad Bioimage Benchmark Collection images
  ☆24Updated 5 years ago
• jump-cellpainting / 2024_Chandrasekaran_NatureMethods
  ☆57Updated 2 weeks ago
• DistributedScience / Distributed-CellProfiler
  Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure.
  ☆40Updated last week
• fish-quant / big-fish
  Toolbox for the analysis of smFISH images.
  ☆58Updated last year
• cytomining / pycytominer
  Python package for processing image-based profiling data
  ☆84Updated this week
• KristinaUlicna / DeepTree
  Jupyter notebooks for deep lineage analysis of single-cell heterogeneity and cell cycling duration heritability.
  ☆30Updated 4 years ago
• angelolab / ark-analysis
  Integrated pipeline for multiplexed image analysis
  ☆79Updated 2 months ago
• KerenLab / CellSighter
  ☆29Updated last year
• AllenCell / aics-segmentation
  Part 1 of Allen Cell and Structure Segmenter: classic image segmentation workflow
  ☆27Updated 5 months ago
• 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…
  ☆33Updated last month
• VasylVaskivskyi / microaligner
  Image registration (alignment) software for large microscopy images
  ☆22Updated last year
• CellProfiler / tutorials
  CellProfiler tutorial pipelines and images
  ☆86Updated 2 months ago
• uhlmanngroup / splinedist
  SplineDist: Automated Cell Segmentation with Spline Curves
  ☆65Updated 3 months ago
• cytomining / DeepProfiler
  Morphological profiling using deep learning
  ☆110Updated 2 months ago
• MannLabs / scPortrait
  ☆36Updated this week
• vanvalenlab / deepcell-label
  Cloud-based data annotation tools for biological images
  ☆77Updated 11 months ago
• Michael-shannon / cellPLATO
  The 2023 version of cellPLATO
  ☆13Updated 2 months ago
• kreshuklab / go-nuclear
  Guides and code for 3D nuclear instance segmentation
  ☆20Updated last week
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆83Updated 2 weeks ago