Alternatives and similar repositories for imaris_extensions:

Users that are interested in imaris_extensions are comparing it to the libraries listed below

• qupath / qupath-extension-align
  QuPath extension to interactively align images
  ☆23Updated 2 weeks ago
• PreibischLab / STIM
  Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.
  ☆27Updated 2 months ago
• saramcardle / FS2K
  Files associated with the From Samples To Knowledge 2025 QuPath training course
  ☆12Updated last week
• niaid / sitk-ibex
  Aligning images acquired with the IBEX microscopy imaging technique
  ☆17Updated 3 months ago
• BodenmillerGroup / readimc
  Python package for reading imaging mass cytometry (IMC) files
  ☆14Updated this week
• emanuega / MERlin
  MERlin is an extensible analysis pipeline applied to decoding MERFISH data
  ☆35Updated 3 years ago
• scverse / napari-spatialdata
  Interactive visualization of spatial omics data
  ☆53Updated this week
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆37Updated last year
• TheJacksonLaboratory / STQ
  Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images
  ☆18Updated 2 months ago
• GuignardLab / napari-sc3D-viewer
  A plugin to visualise 3D spatial single cell omics
  ☆22Updated last year
• nolanlab / SpatialScore
  R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…
  ☆14Updated 3 years ago
• akoyabio / phenoptr
  Helper functions for working with inForm data.
  ☆14Updated 2 years ago
• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆27Updated 7 months ago
• NHPatterson / napari-wsireg
  Whole slide image registration through wsireg in napari.
  ☆13Updated 2 years ago
• oganm / allenBrain
  Acquiring images from allen brain atlas, mouse ISH experiments in R.
  ☆16Updated last year
• BodenmillerGroup / imctools
  Tools to handle IMC data
  ☆23Updated 3 years ago
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆30Updated last year
• HelenaLC / SpatialData
  ☆17Updated last month
• scverse / spatialdata-io
  ☆59Updated this week
• nolanlab / REDSEA
  ☆17Updated last year
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆42Updated last week
• linnarsson-lab / pysmFISH
  Analysis of smFISH data
  ☆11Updated 6 years ago
• AllenInstitute / cell_type_mapper
  Repository for storing prototype functionality implementations for the BKP
  ☆24Updated last week
• alexandrovteam / SpaceM
  ☆15Updated 7 months ago
• labsyspharm / cylinter
  An Interactive Image Segmentation Filter for Multiplex Microscopy
  ☆30Updated 2 months ago
• fmi-basel / glib-nature2018-materials
  Image Processing Package for the Paper "Self-organization and symmetry breaking in intestinal organoid development"
  ☆11Updated 4 years ago
• nolanlab / TissueSchematics
  Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"
  ☆10Updated 2 years ago
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆26Updated 6 months ago
• acycliq / pciSeq
  A probabilistic cell typing algorithm for spatial transcriptomics.
  ☆23Updated 2 weeks ago
• HiDiHlabs / ssam
  ☆28Updated 6 months ago