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.
  ☆68Updated 2 years ago
• DrHanLim / EzColocalization
  ☆12Updated 4 years ago
• rwnull / insitu_probe_generator
  Generate HCR-style Probe Pairs for mRNA visualization
  ☆43Updated 2 years ago
• gustaveroussy / sopa
  Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…
  ☆244Updated this week
• stjude / punctatools
  Detection, colocalization, and quantification of spots / puncta
  ☆14Updated 2 years ago
• scverse / spatialdata
  An open and interoperable data framework for spatial omics data
  ☆329Updated 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…
  ☆230Updated 2 years ago
• scverse / squidpy
  Spatial Single Cell Analysis in Python
  ☆534Updated this week
• spacetx / starfish
  starfish: unified pipelines for image-based transcriptomics
  ☆243Updated this week
• CellProfiler / tutorials
  CellProfiler tutorial pipelines and images
  ☆98Updated 3 weeks ago
• scverse / rapids_singlecell
  rapids_singlecell: GPU-accelerated framework for scRNA analysis
  ☆277Updated this week
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆411Updated 4 months ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆392Updated 2 weeks ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆388Updated 3 months ago
• 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 Slightly outdated but still much liked by learners.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
• vanvalenlab / deepcell-tf
  Deep Learning Library for Single Cell Analysis
  ☆469Updated last year
• broadinstitute / Tangram
  Spatial alignment of single cell transcriptomic data.
  ☆337Updated 4 months ago
• SchmollerLab / Cell_ACDC
  A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data
  ☆186Updated this week
• whitews / FlowKit
  A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces
  ☆191Updated 2 weeks ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆449Updated last year
• STOmics / Stereopy
  A toolkit of spatial transcriptomic analysis.
  ☆266Updated last week
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆397Updated 10 months ago
• BodenmillerGroup / napari-imc
  Imaging Mass Cytometry (IMC) file type support for napari
  ☆12Updated 2 years ago
• Michael-shannon / cellPLATO
  The 2025 version of cellPLATO
  ☆15Updated last month
• kharchenkolab / Baysor
  Bayesian Segmentation of Spatial Transcriptomics Data
  ☆196Updated 11 months ago
• labsyspharm / mcmicro
  Multiple-choice microscopy pipeline
  ☆141Updated this week
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆330Updated 8 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆228Updated last week
• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆235Updated 3 weeks ago
• angelolab / ark-analysis
  Integrated pipeline for multiplexed image analysis
  ☆99Updated 7 months ago