Fiji pipeline for automated serial section reconstruction and mouse brain analysis.
☆31Oct 13, 2023Updated 2 years ago
Alternatives and similar repositories for BrainJ
Users that are interested in BrainJ are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)☆57Apr 29, 2026Updated 3 weeks ago
- Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery☆13Apr 15, 2026Updated last month
- ☆38Mar 22, 2021Updated 5 years ago
- ☆18Feb 10, 2022Updated 4 years ago
- Brainways☆23Aug 28, 2025Updated 8 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- End-to-end light-sheet image analysis for mouse brains, with DL training data generated in VR☆34Jan 2, 2026Updated 4 months ago
- Process images using SimpleITK in napari☆23May 1, 2025Updated last year
- R package for segmentation, registration and generating web-based brain atlases from microscope images☆93Jul 16, 2021Updated 4 years ago
- Blue Brain multi-modal registration and alignment toolbox☆12Feb 14, 2024Updated 2 years ago
- ☆41Mar 4, 2024Updated 2 years ago
- A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.☆123May 6, 2026Updated 2 weeks ago
- Collection of tools to handle Neuropixel 1.0 and 2.0 data☆19May 15, 2026Updated last week
- ☆14Sep 2, 2020Updated 5 years ago
- An open-source ecosystem of hardware and software for head-fixed behavior☆14Sep 25, 2025Updated 8 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- ☆55Aug 30, 2024Updated last year
- A JupyterBook site for napari workshop materials☆10Jul 11, 2022Updated 3 years ago
- Registration to BrainGlobe atlases in napari using Elastix☆29May 5, 2026Updated 3 weeks ago
- This repository contains the code used for the paper "Molecular Atlas of the Adult Mouse Brain".☆16Feb 26, 2021Updated 5 years ago
- High-throughput Detection of Neurons for Brain-wide analysis with Deep Learning☆18Feb 21, 2022Updated 4 years ago
- 3D Extension of the Cellpose Algorithm by Stringer et al., 2021.☆35Oct 10, 2022Updated 3 years ago
- ClearMap 2 with WobblyStitcher, TubeMap and CellMap☆140Apr 23, 2026Updated last month
- Prototype implementation of napari-integrated CNN training viewer☆14Dec 27, 2024Updated last year
- Robust online multiband drift estimation in electrophysiology data☆30Mar 21, 2026Updated 2 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Anatomical space conventions made easy.☆12May 5, 2026Updated 3 weeks ago
- Get Your Brain Together Neuroimage Registration Workshops and Hackathons☆22Nov 14, 2024Updated last year
- ZELDA: a 3D Image Segmentation and Parent to Child relation plugin for microscopy image analysis in napari☆25Nov 25, 2025Updated 6 months ago
- The ANTsX Ecosystem for Mapping the Mouse Brain☆21Dec 2, 2025Updated 5 months ago
- Sample implementation of the MotionMapper behavioral analysis algorithms☆82Sep 8, 2020Updated 5 years ago
- Visualise brainreg registration output☆10Nov 20, 2021Updated 4 years ago
- ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.☆53Jun 18, 2020Updated 5 years ago
- ☆24Feb 12, 2026Updated 3 months ago
- SimBA (Simple Behavioral Analysis), a pipeline and GUI for developing supervised behavioral classifiers☆357Updated this week
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- A python library for advanced lattice light-sheet image analysis☆21Sep 9, 2020Updated 5 years ago
- ☆20Dec 8, 2022Updated 3 years ago
- A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks☆120Updated this week
- miniscope analysis pipeline with interactive visualizations☆98Jul 19, 2024Updated last year
- Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas☆104Updated this week
- Package for automatic post-processing and merging of multiple spike-sorting analyses.☆28Feb 5, 2026Updated 3 months ago
- A GUI built on brainrender: visualise brain regions, neurons and labelled cells.☆12Nov 26, 2020Updated 5 years ago