Alternatives and similar repositories for graph-iss

Users that are interested in graph-iss are comparing it to the libraries listed below

• JaneliaSciComp / multifish
  EASI-FISH analysis pipeline for spatial transcriptomics
  ☆35Updated 8 months ago
• emanuega / MERlin
  MERlin is an extensible analysis pipeline applied to decoding MERFISH data
  ☆35Updated 3 years ago
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year
• GuignardLab / napari-sc3D-viewer
  A plugin to visualise 3D spatial single cell omics
  ☆22Updated last month
• PreibischLab / STIM
  Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.
  ☆29Updated 2 months ago
• PreibischLab / RS-FISH
  Tool for precise, interactive, fast and scalable FISH spot detection
  ☆48Updated 6 months ago
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆47Updated 2 weeks ago
• miti-consortium / MITI
  Minimum Information about Tissue Imaging
  ☆20Updated last year
• vitessce / vitessce-python
  Python API and Jupyter widget for Vitessce
  ☆50Updated last week
• fmi-basel / glib-nature2018-materials
  Image Processing Package for the Paper "Self-organization and symmetry breaking in intestinal organoid development"
  ☆11Updated 4 years ago
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆38Updated 2 years ago
• scverse / spatialdata-io
  ☆65Updated last week
• acycliq / pciSeq
  A probabilistic cell typing algorithm for spatial transcriptomics.
  ☆24Updated last month
• VasylVaskivskyi / microaligner
  Image registration (alignment) software for large microscopy images
  ☆25Updated last year
• saramcardle / FS2K
  Files associated with the From Samples To Knowledge 2025 QuPath training course
  ☆12Updated 3 months ago
• giovp / spatialdata-sandbox
  ☆12Updated 3 months ago
• NHPatterson / napari-wsireg
  Whole slide image registration through wsireg in napari.
  ☆13Updated 2 years ago
• niaid / imaris_extensions
  Algorithmic and Utility Extensions for the Imaris Program
  ☆18Updated 10 months ago
• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆28Updated 10 months ago
• scverse / napari-spatialdata
  Interactive visualization of spatial omics data
  ☆64Updated last week
• beliveau-lab / PaintSHOP_pipeline
  A scalable machine learning pipeline for probe specificity prediction.
  ☆14Updated last year
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆29Updated this week
• wanglab-broad / ClusterMap
  ClusterMap for multi-scale clustering analysis of spatial gene expression
  ☆45Updated last month
• BodenmillerGroup / readimc
  Python package for reading imaging mass cytometry (IMC) files
  ☆15Updated last week
• labsyspharm / cylinter
  An Interactive Image Segmentation Filter for Multiplex Microscopy
  ☆31Updated 6 months ago
• ZhuangLab / MERlin
  MERFISH decoding software
  ☆26Updated 2 years ago
• UFISH-Team / U-FISH
  Deep learning based spot detection for FISH images.
  ☆23Updated last month
• HelenaLC / SpatialData
  ☆17Updated 2 months ago
• multiFISH / EASI-FISH
  Tools and scripts for EASI-FISH image data analysis
  ☆17Updated 2 years ago
• ZhuangLab / MERFISH_analysis
  Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.
  ☆50Updated 4 years ago