Alternatives and similar repositories for BioImager

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

• BiologyTools / BioGTK
  A cross platform version of Bio library & program. Bio is a library & program for annotating, & editing various microscopy imaging format…
  ☆14Updated this week
• petebankhead / imagej-intro
  OUT-OF-DATE! The new book is at https://bioimagebook.github.io
  ☆21Updated 9 years ago
• dmattek / dzPlateViewer
  Deep Zoom Plate Viewer for microscopy images
  ☆18Updated this week
• miura / reproducible_bioimage_analysis
  ☆14Updated 5 years ago
• alxndrkalinin / cubic
  CUDA-accelerated 3D BioImage Computing (ICCV BIC 2025)
  ☆27Updated 2 weeks ago
• CellProfiler / examples
  Example CellProfiler pipelines.
  ☆17Updated 3 years ago
• qupath / qupath-extension-omero-web
  QuPath extension to work with images through OMERO's web API
  ☆10Updated last year
• computationalpathologygroup / pythostitcher
  Python tool for stitching histopathology tissue fragments into artificial whole-mounts.
  ☆23Updated 2 months ago
• MIAnalyzer / MIA
  Microsopic Image Analyzer (MIA)
  ☆28Updated 5 months ago
• pr4deepr / cellpose-colab
  Google Colab notebook for Cellpose
  ☆10Updated 5 months ago
• qupath / qubalab
  Lab for quantitative bioimage analysis experiments in Python
  ☆19Updated this week
• imagej / imagej.github.io
  The ImageJ wiki
  ☆28Updated last week
• bglnelissen / slideToolkit
  slideToolkit: a free toolset for analyzing full size virtual histology slides
  ☆11Updated last year
• 4DNucleome / PartSeg
  Tool for segmentation in bioimaging
  ☆35Updated this week
• royerlab / dexp
  Dataset EXploration & Processing
  ☆33Updated 2 years ago
• AndrewNorgan / wsi
  Open source whole slide image preparation and viewing pipeline
  ☆13Updated 5 years ago
• Ajaxels / MIB2
  Microscopy Image Browser version 2 is a package for image processing, segmentation and visualization of multi-dimensional (2D-4D) microsc…
  ☆36Updated 4 months ago
• psobolewskiPhD / napari_scripts
  Collection of useful (to me) python scripts for interacting with napari
  ☆11Updated 3 years ago
• deepimagej / deepimagej-plugin
  The ImageJ plugin to run deep-learning models
  ☆97Updated 3 months ago
• ahklemm / ImageJMacro_Introduction
  A first intoduction to scripting in Fiji using the ImageJ Macro language.
  ☆26Updated last year
• aelefebv / nellie
  Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
  ☆88Updated 3 weeks ago
• tpecot / WholeSlideImageAnalysisWithQuPath
  ☆30Updated 2 weeks ago
• IDR / idr-metadata
  Curated metadata for all studies published in the Image Data Resource
  ☆16Updated 6 months ago
• marrlab / BaSiC
  A BaSiC Tool for Background and Shading Correction of Optical Microscopy Images
  ☆64Updated 10 months ago
• BaroudLab / Griottes
  Python program to generate NetworkX graphs from segmented images.
  ☆14Updated 2 years ago
• zeiss-microscopy / OAD
  Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools a…
  ☆159Updated 2 weeks ago
• JaneliaSciComp / BigStitcher
  ImgLib2/BDV implementation of Stitching for large datasets
  ☆78Updated 3 months ago
• CellMigrationLab / CellTracksColab
  A platform for compiling, analyzing, and exploring tracking data
  ☆48Updated this week
• clij / clupath
  GPU-accelerated image processing in QuPath
  ☆16Updated 4 years ago
• qupath / qupath-extension-template
  Template to help create a new QuPath extension
  ☆21Updated 5 months ago