Alternatives and similar repositories for Cellpose-Fiji

Users that are interested in Cellpose-Fiji are comparing it to the libraries listed below

• BIOP / ijl-utilities-wrappers
  Wrappers for external software calls (Cellpose, Elastix, Ilastix...) and java utilities (object conversions and display)
  ☆37Updated 2 months ago
• CellMigrationLab / CellTracksColab
  A platform for compiling, analyzing, and exploring tracking data
  ☆46Updated 4 months ago
• kwolbachia / Visualization_toolset
  Imagej toolset to ease hyperstacks visualization and handling
  ☆22Updated 9 months ago
• JaneliaSciComp / multifish
  EASI-FISH analysis pipeline for spatial transcriptomics
  ☆35Updated 8 months ago
• TheJacksonLaboratory / ezomero
  A module with convenience functions for writing Python code that interacts with OMERO.
  ☆45Updated this week
• PreibischLab / RS-FISH
  Tool for precise, interactive, fast and scalable FISH spot detection
  ☆48Updated 6 months ago
• sofroniewn / napari-training-course
  Lectures for a napari training course
  ☆50Updated last year
• grishkam / QuickFigures
  QuickFigures is a toolset for creating scientific figures see publication for details
  ☆35Updated last year
• WhoIsJack / python-bioimage-analysis-tutorial
  A self-explanatory, hands-on intro to bioimage analysis in python. Slightly outdated but still much liked by learners.
  ☆98Updated 2 years ago
• nygctech / PICASSO
  Development of PICASSO plugin for napari
  ☆17Updated 2 years ago
• ahklemm / ImageJMacro_Introduction
  A first intoduction to scripting in Fiji using the ImageJ Macro language.
  ☆26Updated 10 months ago
• RMS-DAIM / Python-for-Bioimage-Analysis
  This is the repository for a Python bioimage analysis course which establishes the fundamentals of image analysis in the context of biolo…
  ☆134Updated 5 years ago
• HenriquesLab / DL4MicEverywhere
  Bringing the ZeroCostDL4Mic experience running everywhere via easy-to-install docker images
  ☆80Updated 3 months ago
• haesleinhuepf / devbio-napari
  ☆51Updated 3 months ago
• Michael-shannon / cellPLATO
  The 2023 version of cellPLATO
  ☆15Updated last week
• weigertlab / spotiflow
  Accurate and efficient spot detection for microscopy data
  ☆92Updated last week
• BiAPoL / imagej-macro-cheat-sheet
  ☆20Updated 4 years ago
• haesleinhuepf / BioImageAnalysisNotebooks
  Python Jupyter notebooks for BioImageAnalysis, GPU-accelerated image processing, bio-image data science and more
  ☆141Updated last month
• saramcardle / FS2K
  Files associated with the From Samples To Knowledge 2025 QuPath training course
  ☆12Updated 3 months ago
• elgw / deconwolf
  Deconvolution of widefield microscopy images and generation of point spread functions
  ☆48Updated 2 weeks ago
• stardist / stardist-napari
  StarDist plugin for napari
  ☆40Updated 11 months ago
• maweigert / spotipy
  ☆12Updated last year
• BiAPoL / PoL-BioImage-Analysis-TS-GPU-Accelerated-Image-Analysis
  PoL Bioimage Analysis Training School: GPU-Accelerated Image Analysis Track
  ☆28Updated last year
• AiviaCommunity / PythonForAivia
  Python scripts library for Aivia. Ask your questions on the forum >>
  ☆15Updated this week
• haesleinhuepf / imagejmacromarkdown
  Generate markdown notebooks from ImageJ Macro
  ☆25Updated 4 years ago
• OakesLab / AFT-Alignment_by_Fourier_Transform
  ☆16Updated last year
• bioimagebook / bioimagebook.github.io
  An introduction to bioimage analysis - http://bioimagebook.github.io
  ☆72Updated last month
• labsyspharm / ashlar
  ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
  ☆144Updated 5 months ago
• kreshuklab / go-nuclear
  Guides and code for 3D nuclear instance segmentation
  ☆22Updated last month
• BiAPoL / napari-clusters-plotter
  A napari plugin for clustering objects according to their properties.
  ☆87Updated last week