neuralib-parser
Data parsers for neuroscience research tools and file formats, providing unified interfaces for segmentation, morphology, imaging, tracking, and confocal microscopy data.
Overview
neuralib-parser provides Python parsers and data structures for output from open-source packages and specific imaging
devices. It includes:
- Segmentation: Cellpose, StarDist cell segmentation
- Morphology: SWC neuron morphology files
- Imaging: Suite2p, Scanbox data formats
- Tracking: DeepLabCut, Facemap behavioral tracking
- Confocal Scans: Zeiss CZI, LSM file formats
Installation
From PyPI
pip install neuralib-parser
With Optional Dependencies
# StarDist support
pip install neuralib-parser[stardist]
# Suite2p integration
pip install neuralib-parser[suite2p]
# Zeiss CZI format support
pip install neuralib-parser[czi]
# Scanbox reader
pip install neuralib-parser[sbx]
# All features
pip install neuralib-parser[all]
From Source (uv recommended)
git clone https://github.com/ytsimon2004/neuralib2.git
cd neuralib2/packages/neuralib-parser
uv pip install -e . # Basic installation
uv pip install -e ".[all]" # With optional features
Requirements
- Python 3.11 or 3.12
- Core dependencies:
neuralib-utils,numpy - See
pyproject.tomlfor optional dependencies
Documentation
- Main Documentation: https://neuralib2.readthedocs.io/
- GitHub Repository: https://github.com/ytsimon2004/neuralib2
- Issue Tracker: https://github.com/ytsimon2004/neuralib2/issues
Important Notes
StarDist and NumPy 2.x
StarDist 0.9.2 supports NumPy 2.x. The stardist extra uses stardist>=0.9.2.
License
BSD 3-Clause License. See LICENSE file for details.
Contributing
Contributions are welcome! Please:
- Fork the repository
- Create a feature branch
- Submit a pull request with clear description
For bug reports and feature requests, use the GitHub issue tracker.
Acknowledgments
This package provides interfaces to:
1 maintainer
Metadata
1 maintainer
Release files for neuralib-parser 0.7.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| neuralib_parser-0.7.2.tar.gz | 40.7 kB | Without provenance | Details for neuralib_parser-0.7.2.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| neuralib_parser-0.7.2-py3-none-any.whl | Python 3 | none | any | Details for neuralib_parser-0.7.2-py3-none-any.whl |
Total release size: 85.9 kB
Release files / neuralib_parser-0.7.2.tar.gz
| Download URL | neuralib_parser-0.7.2.tar.gz |
|---|---|
| Size | 40.7 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
0473c6f377bf4640c7c16466d66e4194ad6badafd6fc96e136959691ad5f9cb3
|
|
BLAKE2b-256 checksum How to use checksums |
dbde399e6afd5f9481eac8e1e792908498f52ef40c90dd51ace21c725b38771c
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
uv/0.11.14 {"installer":{"name":"uv","version":"0.11.14","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
|
Release files / neuralib_parser-0.7.2-py3-none-any.whl
| Download URL | neuralib_parser-0.7.2-py3-none-any.whl |
|---|---|
| Size | 45.1 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
97f65855c5df636fd3a804650a75dbd8f7e11cc3c8f756a175fffc4ee08c4534
|
|
BLAKE2b-256 checksum How to use checksums |
ecab5e41e3ac9174d7456a684999cbf3487cee53d191fdc657e2a2264305247f
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
uv/0.11.14 {"installer":{"name":"uv","version":"0.11.14","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
|
Security for neuralib-parser 0.7.2
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
