A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.
☆120Aug 18, 2025Updated 8 months ago
Alternatives and similar repositories for DeepSlice
Users that are interested in DeepSlice 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)☆57Mar 29, 2026Updated last month
- ImageJ Plugin for Flexible Atlas Segmentation Tool for Multi-Area Processing☆24Jul 4, 2022Updated 3 years ago
- Rendering anatomical heatmaps with brainrender and matplotlib☆51Apr 9, 2026Updated 3 weeks ago
- ABBA, controlled from python☆20Nov 24, 2025Updated 5 months ago
- A 2D-3D histological brain slice registration application for mouse, rat, zebrafish brains.☆39Nov 24, 2023Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Registration to BrainGlobe atlases in napari using Elastix☆30Apr 8, 2026Updated 3 weeks ago
- ☆38Sep 4, 2025Updated 7 months ago
- Automated 3D brain registration with support for multiple species and atlases.☆147Updated this week
- ☆54Aug 30, 2024Updated last year
- A visualization app for 3D-registered data processed in ABBA and QuPath☆20Oct 21, 2022Updated 3 years ago
- A Python interface to access neuroanatomical atlases☆180Updated this week
- ☆46May 21, 2020Updated 5 years ago
- R package for segmentation, registration and generating web-based brain atlases from microscope images☆93Jul 16, 2021Updated 4 years ago
- Framework for predicting neural activity from mouse orofacial movements tracked using a pose estimation model. Package also includes sing…☆191Jan 26, 2026Updated 3 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Fiji pipeline for automated serial section reconstruction and mouse brain analysis.☆31Oct 13, 2023Updated 2 years ago
- Automated 3D cell detection in very large images☆227Apr 16, 2026Updated 2 weeks ago
- Tools to register histological section images and cell count locations to mouse brain atlas☆28May 22, 2022Updated 3 years ago
- ☆19Apr 6, 2022Updated 4 years ago
- MultiModal Big Image Data Sharing and Exploration☆19Jan 13, 2023Updated 3 years ago
- A Python package to visualise neuroanatomical data in atlas space☆641Apr 15, 2026Updated 2 weeks ago
- Calibrated inference of spiking from calcium ΔF/F data using deep networks☆161Feb 11, 2026Updated 2 months ago
- A tool for drawing ROIs on videos and analysing deeplabcut videos.☆35Apr 24, 2026Updated last week
- General information, resources and dicussions for the BrainGlobe project.☆11Feb 21, 2025Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Benchmarking Large Language Models for Bio-Image Analysis Code Generation☆25Nov 21, 2024Updated last year
- ☆18Feb 1, 2024Updated 2 years ago
- Tools to work with Allen Inst CCF data in matlab☆148Jul 15, 2025Updated 9 months ago
- How to use Aligning Big Brains and Atlases with Python☆14May 3, 2023Updated 2 years ago
- Implementation of "Precise Mapping of Single Neurons by Calibrated 3D Reconstruction of Brain Slices Reveals Topographic Projection in Mo…☆16Oct 26, 2022Updated 3 years ago
- Blue Brain multi-modal registration and alignment toolbox☆12Feb 14, 2024Updated 2 years ago
- SimBA (Simple Behavioral Analysis), a pipeline and GUI for developing supervised behavioral classifiers☆357Updated this week
- Process images using SimpleITK in napari☆23May 1, 2025Updated last year
- Hennestad et al. 2022☆23Apr 8, 2026Updated 3 weeks ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Script that registers Histology slices to volumetric image data☆11Oct 4, 2023Updated 2 years ago
- Brainways☆23Aug 28, 2025Updated 8 months ago
- Analysis code for Easy Electrophysiology (www.easyelectrophysiology.com)☆18Mar 20, 2025Updated last year
- Fast spike sorting with drift correction☆608Updated this week
- A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks☆119Mar 9, 2026Updated last month
- Code for the image processing and analysis described our Nature Protocols paper.☆10Jun 26, 2015Updated 10 years ago
- Create 3D/4D animations using a natural language-based syntax☆61Jun 6, 2025Updated 10 months ago