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
- ABBA, controlled from python☆13Updated 3 months 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.☆98Updated 3 weeks ago
- QC and cell type assignment for patch-seq transcriptomics data☆20Updated last year
- ImageJ Plugin for Flexible Atlas Segmentation Tool for Multi-Area Processing☆21Updated 3 years ago
- ☆45Updated 5 years ago
- EASI-FISH analysis pipeline for spatial transcriptomics☆35Updated 7 months ago
- An event-based tool for analyzing and quantifying calcium or neurotransmitter imaging data☆53Updated last year
- ☆34Updated last month
- Semi-manual alignment to reference templates (SMART): An open source pipeline in R for whole brain mapping☆14Updated 3 years ago
- computes intrinsic cell features from intracellular electrophysiology data☆27Updated 8 months ago
- Code for the image processing and analysis described our Nature Protocols paper.☆10Updated 10 years ago
- Automated 3D brain registration with support for multiple species and atlases.☆134Updated last week
- This repository contains the code used for the paper "Molecular Atlas of the Adult Mouse Brain".☆17Updated 4 years ago
- Analysis code for Easy Electrophysiology (www.easyelectrophysiology.com)☆16Updated 3 months ago
- Example vignette for dotdotdot software☆18Updated 4 years ago
- Tools and scripts for EASI-FISH image data analysis☆17Updated 2 years ago
- AICS Segmentation (One-Way) Mirror☆45Updated 4 years ago
- Efficient cell detection in large images using cellfinder in napari☆22Updated last year
- Registration to BrainGlobe atlases in napari using Elastix☆22Updated this week
- 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
- Phenotypic variation of transcriptomic cell types in mouse motor cortex☆26Updated 3 years ago
- Tools for distributed alignment of massive images☆84Updated 3 weeks ago
- Automated 3D cell detection in very large images☆216Updated last week
- Tool for precise, interactive, fast and scalable FISH spot detection☆49Updated 5 months ago
- The ImageJ framework for quantification of neuronal anatomy☆50Updated last week
- A Python interface to access neuroanatomical atlases☆155Updated this week
- A 2D-3D histological brain slice registration application for mouse, rat, zebrafish brains.☆36Updated last year