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IOCBio Sparks: Semi-automatic calcium sparks detection software

Project description

Semi-automatic calcium sparks detection software

IOCBIO Sparks is a cross-platform application for analysis and detection of calcium sparks when imaged using confocal microscope line scanning mode.

IOCBIO Sparks is a free software released under the GNU General Public License (GPL), see the file LICENSE for details.

For testing the software, we have uploaded example datasets at https://sysbio.ioc.ee/software/iocbio-sparks .

Results of the analysis are stored in the database (schema described in docs/database-schema and, if needed, can be exported into spreadsheet file.

Citations and software description

Software is described in a paper published in PeerJ (see below) that gives a background information regarding use of the software and shows an example analysis of sparks. Please cite this paper if you use the software.

Laasmaa, M., Karro, N., Birkedal, R., & Vendelin, M. (2019). IOCBIO Sparks detection and analysis software. PeerJ, 7, e6652 https://doi.org/10.7717/peerj.6652

Installation

There are several ways to install the software. The application requires python3.

For Linux, at present, installation using pip is recommended. It is expected that pip soulution would work for Mac as well.

For Windows, conda solution is recommended for users that don't have Python installed already. Otherwise, if using other than Anaconda Python, consider using pip solution.

pip

To be able to install PyQt5 using pip, you have to use python3.5 or higher. If not available in the system, you can replace pip3 command below with python3 -m pip.

To install published version, run

pip3 install --user iocbio.sparks

This will install all dependencies and it is expected to add a command iocbio-sparks into your PATH. If the command is missing after installation, check whether the default location of pip3 installation is in your path. For Linux, it should be ~/.local/bin.

Its possible to install from Git repository directly:

pip3 install --user git+https://gitlab.com/iocbio/sparks

For development, use

pip3 install --user -e .

in the source directory. To install the current version from the source, use

pip3 install --user .

Note that --user is recommended to avoid messing up the system packages.

conda (Anaconda or Miniconda3)

Here, concise installation instructions are given. For illustrated instructions with screenshots, see Detailed Anaconda instructions

Installation Anaconda

Install Anaconda Python environment by downloading it from https://www.anaconda.com/ . The package uses Python 3 language, so, the version supporting it should be installed. At the moment of writing, its Python 3.6.

Installation of iocbio.sparks

For installation from GUI:

  • Start Anaconda Navigator
  • Add channels by clicking "Channels" on the main screen and adding:
    • conda-forge
    • iocbio
  • icon for iocbio.sparks application should appear on the main Anaconda Navigator. Click on its install for installation.

Please note, it may take several minutes to install the application due to its dependencies.

For installation from CLI, start Anaconda Prompt. In the prompt, add channels:

conda config --append channels conda-forge
conda config --append channels iocbio

and install software

conda install -c iocbio iocbio-sparks

and you are all set.

For running iocbio.sparks in Windows, its possible to start it as an application from Anaconda Navigator or, directly, from starting iocbio-sparks in Anaconda/Scripts directory. For convinience, a shortcut can be created on desktop or Start Menu by the user.

Copyright

Copyright (C) 2018 Laboratory of Systems Biology, Department of Cybernetics, School of Science, Tallinn University of Technology.

Authors:

  • Martin Laasmaa
  • Marko Vendelin

Contact: Marko Vendelin markov@sysbio.ioc.ee

Software license: the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. See LICENSE for details

For any other licenses, please contact the authors.

Project details


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