Alternatives and similar repositories for big-fish

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

• scverse / napari-spatialdata
  Interactive visualization of spatial omics data
  ☆64Updated last week
• JaneliaSciComp / multifish
  EASI-FISH analysis pipeline for spatial transcriptomics
  ☆35Updated 8 months ago
• beliveau-lab / PaintSHOP_pipeline
  A scalable machine learning pipeline for probe specificity prediction.
  ☆14Updated last year
• labsyspharm / mcmicro
  Multiple-choice microscopy pipeline
  ☆136Updated 2 weeks 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 Slightly outdated but still much liked by learners.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
• emanuega / MERlin
  MERlin is an extensible analysis pipeline applied to decoding MERFISH data
  ☆35Updated 3 years ago
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆94Updated last month
• PreibischLab / RS-FISH
  Tool for precise, interactive, fast and scalable FISH spot detection
  ☆48Updated 6 months ago
• Michael-shannon / cellPLATO
  The 2023 version of cellPLATO
  ☆15Updated last week
• angelolab / ark-analysis
  Integrated pipeline for multiplexed image analysis
  ☆93Updated 4 months ago
• labsyspharm / cylinter
  An Interactive Image Segmentation Filter for Multiplex Microscopy
  ☆31Updated this week
• wanglab-broad / ClusterMap
  ClusterMap for multi-scale clustering analysis of spatial gene expression
  ☆46Updated last month
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆38Updated 2 years ago
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆48Updated this week
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆81Updated 2 weeks ago
• TissUUmaps / TissUUmaps
  TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUma…
  ☆59Updated 2 months ago
• HiDiHlabs / ssam
  ☆27Updated 9 months ago
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year
• elgw / deconwolf
  Deconvolution of widefield microscopy images and generation of point spread functions
  ☆49Updated 2 weeks ago
• scverse / spatialdata-io
  ☆66Updated this week
• DrHanLim / EzColocalization
  ☆12Updated 4 years ago
• EliHei2 / segger_dev
  a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…
  ☆74Updated last week
• vitessce / vitessce-python
  Python API and Jupyter widget for Vitessce
  ☆50Updated last week
• glencoesoftware / raw2ometiff
  Raw format to OME-TIFF converter
  ☆55Updated this week
• wahlby-lab / graph-iss
  Graph-based Decoding for In Situ Sequencing
  ☆10Updated 5 years ago
• UFISH-Team / U-FISH
  Deep learning based spot detection for FISH images.
  ☆23Updated this week
• peng-lab / BaSiCPy
  ☆85Updated 4 months ago
• gustaveroussy / sopa
  Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…
  ☆212Updated last week
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆36Updated last year
• CellProfiling / pipex
  A pipeline to transform images into valuable analysis items
  ☆13Updated last month