Alternatives and similar repositories for ClearMap:

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

• ChristophKirst / ClearMap
  ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.
  ☆53Updated 4 years ago
• JaneliaSciComp / bigstream
  Tools for distributed alignment of massive images
  ☆81Updated 3 weeks ago
• brainglobe / slicereg
  A 2D-3D histological brain slice registration application for mouse, rat, zebrafish brains.
  ☆37Updated last year
• brainglobe / brainreg
  Automated 3D brain registration with support for multiple species and atlases.
  ☆134Updated this week
• stegmaierj / Cellpose3D
  3D Extension of the Cellpose Algorithm by Stringer et al., 2021.
  ☆35Updated 2 years ago
• soltanianzadeh / STNeuroNet
  Software for the paper "Fast and robust active neuron segmentation in two-photon calcium imaging using spatio-temporal deep learning," Pr…
  ☆65Updated 5 years ago
• albert597 / TRAILMAP
  ☆45Updated 4 years ago
• nadavyayon / Intensify3D
  Intensify3D is an image normalization tool for large scale fluorescent imaging. It corrects heterogeneities in the signal (defined by the…
  ☆19Updated 4 years ago
• Gubra-ApS / LSFM-mouse-brain-atlas
  ☆18Updated 3 years ago
• PolarBean / DeepSlice
  A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.
  ☆92Updated 3 weeks ago
• vessap / vessap
  Experimental code and examples for: Automated analysis of whole brain vasculature using machine learning
  ☆70Updated 3 years ago
• BIOP / ijp-imagetoatlas
  ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)
  ☆49Updated 2 months ago
• lmbneuron / D-LMBmap
  ☆37Updated last year
• morphonets / SNT
  The ImageJ framework for quantification of neuronal anatomy
  ☆48Updated last week
• PrincetonUniversity / BrainPipe
  ☆18Updated 3 years ago
• seung-lab / DeepEM
  Deep Learning for EM Connectomics
  ☆14Updated 2 years ago
• phflot / flow_registration
  Flow-Registration toolbox for 2P motion compensation
  ☆23Updated 9 months ago
• cgohlke / roifile
  Read and write ImageJ ROI format.
  ☆72Updated 2 months ago
• hadim / read-roi
  Read ROI files .zip or .roi generated with ImageJ.
  ☆53Updated 2 years ago
• cuntzlab / treestoolbox
  TREES toolbox
  ☆28Updated 2 weeks ago
• itsasimiqbal / SeBRe
  Developing a Brain Atlas through Deep Learning
  ☆53Updated last year
• lahammond / BrainJ
  Fiji pipeline for automated serial section reconstruction and mouse brain analysis.
  ☆29Updated last year
• RUB-Bioinf / VesselExpress
  🔬🖥 Automated Blood Vasculature Analysis of 3D Light-Sheet Image Volumes
  ☆47Updated 11 months ago
• StructuralNeurobiologyLab / SyConn
  Toolkit for the generation and analysis of volume eletron microscopy based synaptic connectomes of brain tissue.
  ☆41Updated 10 months ago
• dterstege / FASTMAP
  ImageJ Plugin for Flexible Atlas Segmentation Tool for Multi-Area Processing
  ☆21Updated 2 years ago
• Vaa3D / Vaa3D_Wiki
  www.vaa3d.org
  ☆78Updated 7 years ago
• yu-lab-vt / AQuA
  An event-based tool for analyzing and quantifying calcium or neurotransmitter imaging data
  ☆53Updated 11 months ago
• bahanonu / imaging_tools
  A table containing imaging analysis tools for biology, with a focus on calcium imaging.
  ☆49Updated last year
• 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
• PreibischLab / BigStitcher
  ImgLib2/BDV implementation of Stitching for large datasets
  ☆73Updated last week