Alternatives and similar repositories for whole_brain_analysis

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

• itsasimiqbal / SeBRe
  Developing a Brain Atlas through Deep Learning
  ☆53Updated last year
• JaneliaSciComp / multifish
  EASI-FISH analysis pipeline for spatial transcriptomics
  ☆35Updated 7 months ago
• AllenCell / aics-segmentation
  Part 1 of Allen Cell and Structure Segmenter: classic image segmentation workflow
  ☆26Updated 11 months ago
• cantin-ortiz / molecular-atlas
  This repository contains the code used for the paper "Molecular Atlas of the Adult Mouse Brain".
  ☆17Updated 4 years ago
• mjin1812 / SMART
  Semi-manual alignment to reference templates (SMART): An open source pipeline in R for whole brain mapping
  ☆14Updated 3 years ago
• AllenInstitute / aics-segmentation
  AICS Segmentation (One-Way) Mirror
  ☆45Updated 4 years ago
• AllenCell / aics-ml-segmentation
  ☆32Updated 2 years ago
• stegmaierj / Cellpose3D
  3D Extension of the Cellpose Algorithm by Stringer et al., 2021.
  ☆35Updated 2 years ago
• JaneliaSciComp / bigstream
  Tools for distributed alignment of massive images
  ☆84Updated 3 weeks ago
• BIOP / abba_python
  ABBA, controlled from python
  ☆13Updated 3 months ago
• SystemsResearch / CUBIC_nprot
  Code for the image processing and analysis described our Nature Protocols paper.
  ☆10Updated 10 years ago
• AllenInstitute / open_dataset_tools
  Tools for accessing open data sets published by the Allen Institute for Brain Sciences
  ☆14Updated 4 years ago
• sofroniewn / napari-training-course
  Lectures for a napari training course
  ☆50Updated last year
• morphonets / SNT
  The ImageJ framework for quantification of neuronal anatomy
  ☆50Updated last week
• ABIF-McGill / MethodsJ2
  MethodsJ2
  ☆14Updated 3 years ago
• brainglobe / brainglobe-registration
  Registration to BrainGlobe atlases in napari using Elastix
  ☆22Updated this week
• Gubra-ApS / LSFM-mouse-brain-atlas
  ☆18Updated 3 years ago
• stardist / stardist-napari
  StarDist plugin for napari
  ☆38Updated 10 months ago
• albert597 / TRAILMAP
  ☆45Updated 5 years ago
• ChristophKirst / ClearMap
  ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.
  ☆53Updated 5 years ago
• ActiveBrainAtlas / MouseBrainAtlas
  A system for building mouse brain atlas from histology series
  ☆11Updated 4 years ago
• MouseLand / cellpose-napari
  napari plugin for cellpose (see www.cellpose.org) - an anatomical segmentation tool
  ☆54Updated 8 months ago
• Kapoorlabs-CAPED / NapaTrackMater
  Napari Visualization tool for Trackmate > 6.0 XML files for 2/3D + time tracks. Available via pip package napatrackmater.
  ☆17Updated 2 weeks ago
• RoccoDAnt / napari-zelda
  ZELDA: a 3D Image Segmentation and Parent to Child relation plugin for microscopy image analysis in napari
  ☆20Updated 7 months ago
• BIOP / ijp-imagetoatlas
  ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)
  ☆49Updated last week
• tpecot / WholeSlideImageAnalysisWithQuPath
  ☆26Updated 2 months ago
• ClearAnatomics / ClearMap
  ClearMap 2 with WobblyStitcher, TubeMap and CellMap
  ☆120Updated last month
• maweigert / neubias_academy_stardist
  ☆31Updated 4 years ago
• AllenInstitute / cocoframer
  COmmon COordinate FRAMEwork in R
  ☆36Updated 5 years ago
• wershofe / TWOMBLI
  ☆11Updated last year