IOCBio Sparks: Semi-automatic calcium sparks detection software
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
There are several ways to install the software. The application requires python3.
For Linux, at present, installation using
pip is recommended. It is
pip soulution would work for Mac as well.
conda solution is recommended for users that don't have
Python installed already. Otherwise, if using other than Anaconda
Python, consider using
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
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
If the command is missing after installation, check whether the default location
pip3 installation is in your path. For Linux, it should be
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 .
--user is recommended to avoid messing up the system
conda (Anaconda or Miniconda3)
Here, concise installation instructions are given. For illustrated instructions with screenshots, see Detailed Anaconda instructions
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:
- icon for
iocbio.sparksapplication 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
Anaconda/Scripts directory. For convinience, a
shortcut can be created on desktop or Start Menu by the user.
Copyright (C) 2018 Laboratory of Systems Biology, Department of Cybernetics, School of Science, Tallinn University of Technology.
- Martin Laasmaa
- Marko Vendelin
Contact: Marko Vendelin email@example.com
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.
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
|Filename, size & hash||File type||Python version||Upload date|
|iocbio.sparks-1.1.1.tar.gz (250.5 kB) View hashes||Source||None|