Alternatives and similar repositories for whole_brain_analysis:

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

• AllenCell / aics-segmentation
  Part 1 of Allen Cell and Structure Segmenter: classic image segmentation workflow
  ☆27Updated 5 months ago
• MouseLand / cellpose-napari
  napari plugin for cellpose (see www.cellpose.org) - an anatomical segmentation tool
  ☆48Updated 2 months ago
• ABIF-McGill / MethodsJ2
  MethodsJ2
  ☆14Updated 2 years ago
• AllenCell / aics-ml-segmentation
  ☆30Updated 2 years ago
• AllenInstitute / aics-segmentation
  AICS Segmentation (One-Way) Mirror
  ☆45Updated 4 years ago
• qupath / qupath-extension-instanseg
  The official QuPath extension for InstanSeg
  ☆11Updated last week
• itsasimiqbal / SeBRe
  Developing a Brain Atlas through Deep Learning
  ☆51Updated last year
• ksugar / qupath-extension-cellsparse
  QuPath extension for Cellsparse
  ☆17Updated last month
• tpecot / WholeSlideImageAnalysisWithQuPath
  ☆24Updated 4 months ago
• AllenInstitute / open_dataset_tools
  Tools for accessing open data sets published by the Allen Institute for Brain Sciences
  ☆11Updated 3 years ago
• Gubra-ApS / LSFM-mouse-brain-atlas
  ☆18Updated 2 years ago
• wershofe / TWOMBLI
  ☆10Updated 10 months ago
• stegmaierj / Cellpose3D
  3D Extension of the Cellpose Algorithm by Stringer et al., 2021.
  ☆32Updated 2 years ago
• JaneliaSciComp / multifish
  EASI-FISH analysis pipeline for spatial transcriptomics
  ☆33Updated 2 months ago
• nygctech / PICASSO
  Development of PICASSO plugin for napari
  ☆14Updated 2 years ago
• stardist / augmend
  simple package for augmentation of n-dimensional arrays
  ☆32Updated last year
• ariel-waisman / LabelsToROIs
  A Fiji/ImageJ plugin to generate ROIs from label images, allowing ROI erosion and quantification
  ☆22Updated 3 years ago
• oanegros / Blender_for_Biologists_2023
  ☆38Updated 5 months ago
• embl-cba / elastixWrapper
  ☆13Updated 2 years ago
• kreshuklab / MorphoFeatures
  MorphoFeatures code and data
  ☆19Updated last year
• stardist / stardist-napari
  StarDist plugin for napari
  ☆36Updated 4 months ago
• BIOP / qupath-groovy-python-runner
  A proof of concept to run python segmentations and recovering the results within QuPath
  ☆19Updated 3 years ago
• ActiveBrainAtlas / MouseBrainAtlas
  A system for building mouse brain atlas from histology series
  ☆11Updated 4 years ago
• imjoy-team / example-plugins
  ☆15Updated 4 years ago
• MIAnalyzer / MIA
  Microsopic Image Analyzer (MIA)
  ☆29Updated 9 months ago
• TheJacksonLaboratory / dask_relabeling
  A relabeling tool for tiled segmentation with Dask
  ☆12Updated 3 months ago
• BIOP / EasyXT-FIJI
  Commands and Classes for interfacing between Imaris and Fiji
  ☆12Updated 3 months ago
• Kapoorlabs-CAPED / NapaTrackMater
  Napari Visualization tool for Trackmate > 6.0 and bTrackmate XML files for 2/3D + time tracks. Available via pip package napatrackmater.
  ☆16Updated last month
• clij / clupath
  GPU-accelerated image processing in QuPath
  ☆15Updated 3 years ago
• maweigert / neubias_academy_stardist
  ☆28Updated 3 years ago