Alternatives and similar repositories for big-fish-examples

Users that are interested in big-fish-examples are comparing it to the libraries listed below

• fish-quant / big-fish
  Toolbox for the analysis of smFISH images.
  ☆67Updated last year
• DrHanLim / EzColocalization
  ☆12Updated 4 years ago
• stjude / punctatools
  Detection, colocalization, and quantification of spots / puncta
  ☆13Updated 2 years ago
• scverse / spatialdata
  An open and interoperable data framework for spatial omics data
  ☆302Updated this week
• BiAPoL / Bio-image_Analysis_with_Python
  Lecture materials "Bio-image analysis, biostatistics, programming and machine learning for computational biology" at the Center of Molecu…
  ☆222Updated last year
• scverse / squidpy
  Spatial Single Cell Analysis in Python
  ☆507Updated this week
• gustaveroussy / sopa
  Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…
  ☆222Updated this week
• rwnull / insitu_probe_generator
  Generate HCR-style Probe Pairs for mRNA visualization
  ☆38Updated 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 Slightly outdated but still much liked by learners.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
• spacetx / starfish
  starfish: unified pipelines for image-based transcriptomics
  ☆237Updated 3 weeks ago
• BioImaging-NKI / Foci-analyzer
  ImageJ macro for the analysis of foci (e.g. DNA damage) in nuclei/cells
  ☆19Updated last week
• vanvalenlab / deepcell-tf
  Deep Learning Library for Single Cell Analysis
  ☆463Updated last year
• Michael-shannon / cellPLATO
  The 2025 version of cellPLATO
  ☆15Updated this week
• SchmollerLab / Cell_ACDC
  A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data
  ☆178Updated this week
• peng-lab / BaSiCPy
  ☆87Updated 5 months ago
• cbib / DeepSpot
  DeepSpot is a deep learning method for the enhancement of mRNA fluorescent spots in microscopy images
  ☆14Updated 3 years ago
• elgw / deconwolf
  Deconvolution of widefield microscopy images and generation of point spread functions
  ☆49Updated last week
• scverse / rapids_singlecell
  rapids_singlecell: GPU-accelerated framework for scRNA analysis
  ☆234Updated last week
• 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…
  ☆135Updated 5 years ago
• CellProfiler / tutorials
  CellProfiler tutorial pipelines and images
  ☆93Updated 3 weeks ago
• whitews / FlowKit
  A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces
  ☆186Updated 2 months ago
• BIOP / qupath-extension-cellpose
  an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.
  ☆77Updated 3 weeks ago
• JaneliaSciComp / multifish
  EASI-FISH analysis pipeline for spatial transcriptomics
  ☆35Updated 9 months ago
• trackmate-sc / TrackMate
  TrackMate is your buddy for your everyday tracking.
  ☆207Updated last week
• weigertlab / spotiflow
  Accurate and efficient spot detection for microscopy data
  ☆95Updated 3 weeks ago
• guiwitz / neubias_academy_biapy
  NEUBIAS Academy @Home: Interactive Bioimage Analysis with Python and Jupyter
  ☆63Updated 2 years ago
• beliveau-lab / PaintSHOP_pipeline
  A scalable machine learning pipeline for probe specificity prediction.
  ☆14Updated last year
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆375Updated 7 months ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆438Updated 9 months ago
• scverse / napari-spatialdata
  Interactive visualization of spatial omics data
  ☆64Updated this week