Alternatives and similar repositories for ClearMap:

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

• BIOP / ijp-imagetoatlas
  ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)
  ☆49Updated this week
• brainglobe / slicereg
  A 2D-3D histological brain slice registration application for mouse, rat, zebrafish brains.
  ☆37Updated last year
• nel-lab / FIOLA
  ☆33Updated last year
• lahammond / BrainJ
  Fiji pipeline for automated serial section reconstruction and mouse brain analysis.
  ☆29Updated last year
• PrincetonUniversity / BrainPipe
  ☆18Updated 3 years ago
• ClearAnatomics / ClearMap
  ClearMap 2 with WobblyStitcher, TubeMap and CellMap
  ☆119Updated this week
• Gubra-ApS / LSFM-mouse-brain-atlas
  ☆18Updated 2 years ago
• dterstege / FASTMAP
  ImageJ Plugin for Flexible Atlas Segmentation Tool for Multi-Area Processing
  ☆20Updated 2 years ago
• albert597 / TRAILMAP
  ☆45Updated 4 years ago
• JaneliaSciComp / bigstream
  Tools for distributed alignment of massive images
  ☆80Updated this week
• PolarBean / DeepSlice
  A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.
  ☆91Updated 3 months ago
• wildrootlab / SHARCQ
  Tools to register histological section images and cell count locations to mouse brain atlas
  ☆25Updated 2 years ago
• bkntr / brainways
  Brainways
  ☆15Updated last month
• 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 3 months ago
• AllenInstitute / cocoframer
  COmmon COordinate FRAMEwork in R
  ☆36Updated 4 years ago
• bahanonu / imaging_tools
  A table containing imaging analysis tools for biology, with a focus on calcium imaging.
  ☆46Updated last year
• brainglobe / brainreg
  Automated 3D brain registration with support for multiple species and atlases.
  ☆130Updated last week
• brainglobe / brainglobe-napari-io
  Read and write files from the BrainGlobe neuroanatomy suite
  ☆13Updated last week
• zhoupc / OASIS_matlab
  ☆34Updated 3 years ago
• cogilab / AMaSiNe
  Implementation of "Precise Mapping of Single Neurons by Calibrated 3D Reconstruction of Brain Slices Reveals Topographic Projection in Mo…
  ☆14Updated 2 years ago
• tractatus / wholebrain
  R package for segmentation, registration and generating web-based brain atlases from microscope images
  ☆87Updated 3 years ago
• DeNardoLab / BehaviorDEPOT
  Repository for BehaviorDEPOT pipeline app files and source code
  ☆36Updated 4 months ago
• brainglobe / cellfinder-napari
  Efficient cell detection in large images using cellfinder in napari
  ☆23Updated last year
• phflot / flow_registration
  Flow-Registration toolbox for 2P motion compensation
  ☆22Updated 6 months ago
• neurodata / CloudReg
  CloudReg
  ☆11Updated 10 months ago
• owenrandlett / Z-Brain
  Z-Brain Viewer and Analysis Scripts for MAP-Mapping
  ☆22Updated 6 years ago
• petersaj / AP_histology
  Histology processing
  ☆65Updated 10 months ago
• NTCColumbia / moco
  motion correction
  ☆16Updated 2 years ago
• cuntzlab / treestoolbox
  TREES toolbox
  ☆27Updated 4 months ago