Alternatives and similar repositories for tissue_miner:

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

• blaineylab / OpticalPooledScreens
  ☆13Updated 2 years ago
• hms-dbmi / brainmapr
  R package to infer spatial location of neuronal subpopulations within the developing mouse brain by integrating single-cell RNA-seq data …
  ☆17Updated 9 years ago
• zjniu / Piscis
  An automatic deep learning algorithm for spot detection in fluorescence microscopy images.
  ☆17Updated last month
• fmi-basel / glib-nature2018-materials
  Image Processing Package for the Paper "Self-organization and symmetry breaking in intestinal organoid development"
  ☆11Updated 4 years ago
• AllenInstitute / cell_type_mapper
  Repository for storing prototype functionality implementations for the BKP
  ☆22Updated 2 weeks ago
• alexandrovteam / SpaceM
  ☆13Updated 5 months ago
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆34Updated last year
• feldman4 / OpticalPooledScreens_2019
  Examples and code for optical pooled screens
  ☆10Updated 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.
  ☆25Updated 4 months ago
• JEFworks-Lab / MERmaid
  WebGL-based viewer for spatially-resolved transcriptomics data
  ☆26Updated 2 years ago
• scverse / spatialdata-io
  ☆48Updated this week
• wahlby-lab / graph-iss
  Graph-based Decoding for In Situ Sequencing
  ☆10Updated 4 years ago
• vitessce / vitessce-python
  Python API and Jupyter widget for Vitessce
  ☆43Updated 2 weeks ago
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆62Updated last week
• theislab / interactive_plotting
  ☆21Updated 4 years ago
• GuignardLab / napari-sc3D-viewer
  A plugin to visualise 3D spatial single cell omics
  ☆22Updated 10 months ago
• PreibischLab / STIM
  Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.
  ☆26Updated 3 weeks ago
• beliveau-lab / PaintSHOP_pipeline
  A scalable machine learning pipeline for probe specificity prediction.
  ☆13Updated last year
• miti-consortium / MITI
  Minimum Information about Tissue Imaging
  ☆20Updated last year
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated 9 months ago
• ZhuangLab / MERFISH_analysis
  Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.
  ☆50Updated 3 years ago
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆25Updated 4 months ago
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆38Updated this week
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆52Updated 8 months ago
• VasylVaskivskyi / microaligner
  Image registration (alignment) software for large microscopy images
  ☆22Updated last year
• BodenmillerGroup / imctools
  Tools to handle IMC data
  ☆23Updated 2 years ago
• broadchenf / Slideseq
  ☆11Updated 6 years ago
• linnarsson-lab / pysmFISH
  Analysis of smFISH data
  ☆11Updated 6 years ago
• AllenInstitute / mfishtools
  Building Gene Sets and Mapping mFISH Data
  ☆16Updated last year