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.
To avoid interference with the other packages, it is recommended to use virtual environments, as described below.
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 with virtual environment
Sometimes packages for different applications can cause incompatibilities. To avoid it, you could use virtual environment for the software installation. To create virtual python environment, run
python -m venv iocbio-sparks
This will create folder iocbio-sparks
and install scripts, such as
pip
, into it. To use the environment, call pip
from that folder
and install iocbio-sparks into it
iocbio-sparks/bin/pip install iocbio.sparks
and run by
iocbio-sparks/bin/iocbio-sparks
Same in Windows, using Anaconda Python PowerShell:
python.exe -m venv iocbio-sparks
.\iocbio-sparks\Scripts\python.exe
.\iocbio-sparks\Scripts\pip install iocbio.sparks
and use by
.\iocbio-sparks\Scripts\Activate.ps1
iocbio-sparks.exe
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
We have recently (Jun 2021) seen issues with the resolution of dependencies by Anaconda fresh install. For new users, we recommend to install Anaconda (below) and proceed with either installation using virtual environment by pip (above) or virtual conda environment (below).
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 in conda virtual environment
To avoid conflicts with Anaconda GUI and other packages, it is recommended to setup separate environment for IOCBIO Sparks. In Windows, start Anaconda PowerShell and run
conda create --name iocbio-sparks
Ignore the warning regarding a space in environment path and proceed with creating it.
Next, activate the environment and install the channels:
conda activate iocbio-sparks
conda config --append channels conda-forge
conda config --append channels iocbio
and install software
conda install -c iocbio iocbio.sparks
To run, from activated environment, call
iocbio-sparks.exe
Installation of iocbio.sparks - main environment
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.
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