tractatus / wholebrainLinks
R package for segmentation, registration and generating web-based brain atlases from microscope images
☆88Updated 4 years ago
Alternatives and similar repositories for wholebrain
Users that are interested in wholebrain are comparing it to the libraries listed below
Sorting:
- COmmon COordinate FRAMEwork in R☆36Updated 5 years ago
- ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.☆53Updated 5 years ago
- EASI-FISH analysis pipeline for spatial transcriptomics☆35Updated 9 months ago
- ☆45Updated 5 years ago
- ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)☆52Updated last week
- ABBA, controlled from python☆15Updated 2 weeks ago
- A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.☆105Updated last week
- Code for the image processing and analysis described our Nature Protocols paper.☆10Updated 10 years ago
- ImageJ Plugin for Flexible Atlas Segmentation Tool for Multi-Area Processing☆23Updated 3 years ago
- Analysis code for Easy Electrophysiology (www.easyelectrophysiology.com)☆17Updated 5 months ago
- The ImageJ framework for quantification of neuronal anatomy☆50Updated last week
- AICS Segmentation (One-Way) Mirror☆45Updated 4 years ago
- QC and cell type assignment for patch-seq transcriptomics data☆20Updated last year
- This is the repository for a Python bioimage analysis course which establishes the fundamentals of image analysis in the context of biolo…☆135Updated 5 years ago
- Registration to BrainGlobe atlases in napari using Elastix☆22Updated last week
- Automated 3D brain registration with support for multiple species and atlases.☆136Updated 3 weeks ago
- Tools for distributed alignment of massive images☆86Updated this week
- Lectures for a napari training course☆50Updated 2 years ago
- Automated 3D cell detection in very large images☆217Updated 3 weeks ago
- Semi-manual alignment to reference templates (SMART): An open source pipeline in R for whole brain mapping☆14Updated 3 years ago
- ☆34Updated 3 months ago
- This repository contains the code used for the paper "Molecular Atlas of the Adult Mouse Brain".☆16Updated 4 years ago
- Tool for precise, interactive, fast and scalable FISH spot detection☆49Updated 6 months ago
- ☆18Updated 3 years ago
- computes intrinsic cell features from intracellular electrophysiology data☆27Updated this week
- Generate markdown notebooks from ImageJ Macro☆25Updated 4 years ago
- An event-based tool for analyzing and quantifying calcium or neurotransmitter imaging data☆53Updated last year
- A self-explanatory, hands-on intro to bioimage analysis in python. Slightly outdated but still much liked by learners.☆98Updated 2 years ago
- A 2D-3D histological brain slice registration application for mouse, rat, zebrafish brains.☆36Updated last year
- A visualization app for 3D-registered data processed in ABBA and QuPath☆18Updated 2 years ago