lahammond / BrainJLinks
Fiji pipeline for automated serial section reconstruction and mouse brain analysis.
☆29Updated last year
Alternatives and similar repositories for BrainJ
Users that are interested in BrainJ are comparing it to the libraries listed below
Sorting:
- ☆52Updated last year
- Repository for BehaviorDEPOT pipeline app files and source code☆38Updated 11 months ago
- A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.☆105Updated last month
- Brainways☆21Updated 3 weeks ago
- Rendering anatomical heatmaps with brainrender and matplotlib☆44Updated 2 weeks ago
- Histology processing☆69Updated last week
- Automated 3D cell detection in very large images☆218Updated 2 weeks ago
- Automated 3D brain registration with support for multiple species and atlases.☆136Updated 2 weeks ago
- A table containing imaging analysis tools for biology, with a focus on calcium imaging.☆52Updated 2 years ago
- A Python interface to access neuroanatomical atlases☆157Updated this week
- ☆18Updated 3 years ago
- Platform for Calcium Imaging analysis. DEPRECATED.☆62Updated last year
- miniscope analysis pipeline with interactive visualizations☆95Updated last year
- ☆34Updated 4 months ago
- ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.☆53Updated 5 years ago
- a napari plugin for labeling and refining keypoint data within DeepLabCut projects☆57Updated 3 weeks ago
- Fiber Photometry Modular Analysis Tool Suite☆40Updated 4 years ago
- Calibrated inference of spiking from calcium ΔF/F data using deep networks☆151Updated 3 weeks ago
- Match suite2p ROIs between imaging sessions☆27Updated 6 years ago
- CIAtah (pronounced cheetah): a software package for calcium imaging analysis of one- and two-photon imaging datasets. Documentation: http…☆95Updated 10 months ago
- Tools to register histological section images and cell count locations to mouse brain atlas☆28Updated 3 years ago
- Registration of cells across sessions.☆75Updated last year
- High level pandas-based API for batch analysis of Calcium Imaging data using CaImAn☆69Updated 2 weeks ago
- Calcium Data Extraction and Analysis☆45Updated 2 years ago
- A gui for browsing joint calcium imaging + behavioral data.☆54Updated 7 months ago
- Implementation of "Precise Mapping of Single Neurons by Calibrated 3D Reconstruction of Brain Slices Reveals Topographic Projection in Mo…☆15Updated 2 years ago
- ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)☆52Updated last week
- Bonsai package for controlling headborne, calcium imaging miniscopes☆12Updated last year
- Serial-section automated anatomy extension for ScanImage☆15Updated last month
- EXTRACT is a tractable and robust automated cell extraction tool for calcium imaging, which extracts the activities of cells as time seri…☆77Updated 9 months ago