Alternatives and similar repositories for wholebrain:

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

• AllenInstitute / cocoframer
  COmmon COordinate FRAMEwork in R
  ☆36Updated 4 years ago
• ChristophKirst / ClearMap
  ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.
  ☆52Updated 4 years ago
• BIOP / ijp-imagetoatlas
  ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)
  ☆49Updated last week
• AllenInstitute / patchseqtools
  QC and cell type assignment for patch-seq transcriptomics data
  ☆19Updated 10 months ago
• AllenInstitute / ipfx
  computes intrinsic cell features from intracellular electrophysiology data
  ☆27Updated 4 months ago
• dterstege / FASTMAP
  ImageJ Plugin for Flexible Atlas Segmentation Tool for Multi-Area Processing
  ☆21Updated 2 years ago
• LieberInstitute / dotdotdot
  Example vignette for dotdotdot software
  ☆18Updated 3 years ago
• PolarBean / DeepSlice
  A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.
  ☆91Updated this week
• albert597 / TRAILMAP
  ☆45Updated 4 years ago
• SystemsResearch / CUBIC_nprot
  Code for the image processing and analysis described our Nature Protocols paper.
  ☆10Updated 9 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
• nel-lab / FIOLA
  ☆34Updated last year
• AllenInstitute / aics-segmentation
  AICS Segmentation (One-Way) Mirror
  ☆45Updated 4 years ago
• brainglobe / brainreg
  Automated 3D brain registration with support for multiple species and atlases.
  ☆132Updated this week
• yu-lab-vt / AQuA
  An event-based tool for analyzing and quantifying calcium or neurotransmitter imaging data
  ☆53Updated 10 months ago
• bf777 / MesoNet
  A python toolbox for locating and exporting brain regions from mouse brain images.
  ☆12Updated 4 months ago
• JaneliaSciComp / multifish
  EASI-FISH analysis pipeline for spatial transcriptomics
  ☆33Updated 3 months ago
• morphonets / SNT
  The ImageJ framework for quantification of neuronal anatomy
  ☆46Updated this week
• easy-electrophysiology / easy-electrophysiology-analysis
  Analysis code for Easy Electrophysiology (www.easyelectrophysiology.com)
  ☆16Updated 4 months ago
• argunsah / SpineS
  Dendritic Spine Analysis Software
  ☆13Updated last year
• PrincetonUniversity / BrainPipe
  ☆18Updated 3 years ago
• AllenInstitute / MIES
  Multichannel Igor Electrophysiology Suite
  ☆25Updated this week
• berenslab / mini-atlas
  Phenotypic variation of transcriptomic cell types in mouse motor cortex
  ☆24Updated 3 years ago
• multiFISH / EASI-FISH
  Tools and scripts for EASI-FISH image data analysis
  ☆17Updated 2 years ago
• lahammond / BrainJ
  Fiji pipeline for automated serial section reconstruction and mouse brain analysis.
  ☆29Updated last year
• natverse / natverse
  Umbrella package to help install/load nat packages
  ☆10Updated 3 years ago
• JaneliaSciComp / bigstream
  Tools for distributed alignment of massive images
  ☆80Updated last month
• Tyelab / HMMGLM
  The code for the Hidden Markov Model Generalized Linear Model used to model discrete complex behavior profiles of mice using neural activ…
  ☆10Updated 2 years ago
• petersaj / AP_histology
  Histology processing
  ☆65Updated this week
• brainglobe / brainglobe-atlasapi
  A Python interface to access neuroanatomical atlases
  ☆135Updated this week