ChristophKirst / ClearMap
ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.
☆53Updated 4 years ago
Alternatives and similar repositories for ClearMap:
Users that are interested in ClearMap are comparing it to the libraries listed below
- Fiji pipeline for automated serial section reconstruction and mouse brain analysis.☆29Updated last year
- ☆18Updated 3 years ago
- ☆45Updated 4 years ago
- ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)☆49Updated 2 weeks ago
- A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.☆91Updated last week
- Automated 3D brain registration with support for multiple species and atlases.☆133Updated last week
- ☆18Updated 2 years ago
- Tools for distributed alignment of massive images☆81Updated last month
- ☆34Updated last year
- Tools to register histological section images and cell count locations to mouse brain atlas☆25Updated 2 years ago
- ClearMap 2 with WobblyStitcher, TubeMap and CellMap☆119Updated this week
- A 2D-3D histological brain slice registration application for mouse, rat, zebrafish brains.☆37Updated last year
- An event-based tool for analyzing and quantifying calcium or neurotransmitter imaging data☆53Updated 10 months ago
- Implementation of "Precise Mapping of Single Neurons by Calibrated 3D Reconstruction of Brain Slices Reveals Topographic Projection in Mo…☆14Updated 2 years ago
- COmmon COordinate FRAMEwork in R☆36Updated 4 years ago
- ☆51Updated 6 months ago
- A table containing imaging analysis tools for biology, with a focus on calcium imaging.☆48Updated last year
- Repository for BehaviorDEPOT pipeline app files and source code☆36Updated 5 months ago
- Analysis code for Easy Electrophysiology (www.easyelectrophysiology.com)☆16Updated this week
- motion correction☆17Updated 2 years ago
- Rendering anatomical heatmaps with brainrender and matplotlib☆38Updated 2 weeks ago
- ImageJ Plugin for Flexible Atlas Segmentation Tool for Multi-Area Processing☆21Updated 2 years ago
- Platform for Calcium Imaging analysis. DEPRECATED.☆60Updated last year
- A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks☆80Updated last month
- Histology processing☆65Updated last week
- Brainways☆16Updated last week
- Calcium Data Extraction and Analysis☆43Updated 2 years ago
- BIRDS plug-in on Fiji and attached jar package☆18Updated 3 years ago
- A python toolbox for locating and exporting brain regions from mouse brain images.☆12Updated 4 months ago
- A tool for manual pointwise deformable registration using bigdataviewer.☆27Updated last month