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slap2-utils

slap2-utils: Tools for Processing SLAP2 Data - Published in JOSS (2025)

https://github.com/peter-hogg/slap2_utils

Science Score: 93.0%

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    CITATION.cff file
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    Found 1 DOI reference(s) in JOSS metadata
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    JOSS paper metadata
    Published in Journal of Open Source Software
Last synced: 6 months ago · JSON representation

Repository

SLAP2 Helper Functions

Basic Info
  • Host: GitHub
  • Owner: Peter-Hogg
  • License: mpl-2.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 285 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 2
  • Open Issues: 0
  • Releases: 2
Created over 2 years ago · Last pushed 7 months ago
Metadata Files
Readme License

README.md

slap2-utils

TestsDocumentation

Overview

The slap2-utils library is designed to facilitate the reading of SLAP2 (Scanned Line Angular Projection Microscopy version 2) binary files using Python. This utility aims to support researchers and developers working with data from SLAP2 two-photon microscopes by providing an interface to manipulate and analyze these files directly in Python as an alternative to a Matlab-based workflow. The SLAP2 microscope is a commercially available kit from MBF Bioscience (https://www.mbfbioscience.com/products/slap2). The detailed documentation can be found by clicking the documentation icon above Overview.

Features

  • Reading SLAP2 Binary Files: Convert SLAP2 proprietary binary data into accessible formats for Python.
  • Metadata Parsing: Extract and utilize metadata associated with SLAP2 data files.
  • Data Manipulation: Tools to manipulate and process data points read from the binary file.
  • Trace Extraction: Tools to extract and generate traces from ROIs imaged in integrated scan mode.
  • Data Inspection: A GUI to inspect and review data stored in the binary file.

Installation

Install with pip bash pip install slap2-utils

Clone this repository

bash git clone https://github.com/Peter-Hogg/SLAP2_Utils.git

Contributing

Contributions are welcome! If you'd like to contribute, please fork the repository and use a new branch for your contributions. Pull requests are welcome. Please report bugs, as we're still refining this library over time.

License

This project is licensed under the Mozilla Public License Version 2.0 - see the LICENSE.md file for details.

Credits and Acknowledgements

This library was developed by Peter Hogg and Jerry Tong. It's a rework of several Matlab tools from MBF with added utility functions. Thanks to all contributors who have helped in refining this tool and helped with the project.

Owner

  • Name: Peter
  • Login: Peter-Hogg
  • Kind: user
  • Location: University Of British Columbia

JOSS Publication

slap2-utils: Tools for Processing SLAP2 Data
Published
August 20, 2025
DOI
Volume 10, Issue 112, Page 8054
Authors
Peter William Hogg
Department of Cellular and Physiological Sciences, Centre for Brain Health, School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
Jerry Shijie Tong ORCID
Department of Cellular and Physiological Sciences, Centre for Brain Health, School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
Kurt Haas
Department of Cellular and Physiological Sciences, Centre for Brain Health, School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
Editor
Kevin M. Moerman ORCID
Tags
neuroscience microscopy calcium imaging voltage imaging
View PDF Review Thread Software Archive

GitHub Events

Total
  • Create event: 17
  • Release event: 1
  • Issues event: 4
  • Watch event: 1
  • Delete event: 5
  • Issue comment event: 9
  • Push event: 43
  • Pull request event: 5
Last Year
  • Create event: 17
  • Release event: 1
  • Issues event: 4
  • Watch event: 1
  • Delete event: 5
  • Issue comment event: 9
  • Push event: 43
  • Pull request event: 5

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 8
  • Average time to close issues: 25 days
  • Average time to close pull requests: 1 day
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 2.5
  • Average comments per pull request: 1.5
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 8
  • Average time to close issues: 25 days
  • Average time to close pull requests: 1 day
  • Issue authors: 2
  • Pull request authors: 3
  • Average comments per issue: 2.5
  • Average comments per pull request: 1.5
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • larsenkg (1)
  • jrkerns (1)
Pull Request Authors
  • m-xie (4)
  • Peter-Hogg (2)
  • j-friedrich (2)
Top Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 78 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 22
  • Total maintainers: 1
pypi.org: slap2-utils

Code to support using a SLAP2 Microscope

  • Versions: 22
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 78 Last month
Rankings
Dependent packages count: 9.5%
Average: 36.1%
Dependent repos count: 62.7%
Maintainers (1)
neuropete
Last synced: 6 months ago