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 5 years ago
• ChristophKirst / ClearMap
  ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.
  ☆53Updated 4 years ago
• BIOP / ijp-imagetoatlas
  ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)
  ☆49Updated 3 months ago
• AllenInstitute / ipfx
  computes intrinsic cell features from intracellular electrophysiology data
  ☆27Updated 7 months ago
• PolarBean / DeepSlice
  A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.
  ☆96Updated last month
• multiFISH / EASI-FISH
  Tools and scripts for EASI-FISH image data analysis
  ☆17Updated 2 years ago
• AllenInstitute / MIES
  Multichannel Igor Electrophysiology Suite
  ☆27Updated this week
• BIOP / abba_python
  ABBA, controlled from python
  ☆13Updated 2 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 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
• berenslab / mini-atlas
  Phenotypic variation of transcriptomic cell types in mouse motor cortex
  ☆25Updated 3 years ago
• AllenInstitute / patchseqtools
  QC and cell type assignment for patch-seq transcriptomics data
  ☆20Updated last year
• SystemsResearch / CUBIC_nprot
  Code for the image processing and analysis described our Nature Protocols paper.
  ☆10Updated 9 years ago
• PrincetonUniversity / BrainPipe
  ☆18Updated 3 years ago
• JaneliaSciComp / multifish
  EASI-FISH analysis pipeline for spatial transcriptomics
  ☆35Updated 6 months ago
• 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.
  ☆134Updated this week
• JaneliaSciComp / bigstream
  Tools for distributed alignment of massive images
  ☆81Updated last month
• yu-lab-vt / AQuA
  An event-based tool for analyzing and quantifying calcium or neurotransmitter imaging data
  ☆53Updated last year
• nel-lab / FIOLA
  ☆34Updated 2 weeks ago
• wildrootlab / SHARCQ
  Tools to register histological section images and cell count locations to mouse brain atlas
  ☆26Updated 3 years ago
• natverse / natverse
  Umbrella package to help install/load nat packages
  ☆11Updated 3 years ago
• morphonets / SNT
  The ImageJ framework for quantification of neuronal anatomy
  ☆49Updated this week
• easy-electrophysiology / easy-electrophysiology-analysis
  Analysis code for Easy Electrophysiology (www.easyelectrophysiology.com)
  ☆16Updated 2 months ago
• AllenInstitute / abc_atlas_access
  Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas
  ☆76Updated last week
• RMS-DAIM / Python-for-Bioimage-Analysis
  This is the repository for a Python bioimage analysis course which establishes the fundamentals of image analysis in the context of biolo…
  ☆134Updated 5 years ago
• petersaj / AP_histology
  Histology processing
  ☆65Updated last month
• lahammond / BrainJ
  Fiji pipeline for automated serial section reconstruction and mouse brain analysis.
  ☆29Updated last year
• tensionhead / pyBOAT
  A Biological Oscillations Analysis Toolkit
  ☆20Updated last week