Software for analysis of sequential imaging data
Project description
Overview
SIMA (Sequential IMage Analysis) is an Open Source package for analysis of time-series imaging data arising from fluorescence microscopy. The functionality of this package includes:
correction of motion artifacts
segmentation of imaging fields into regions of interest (ROIs)
extraction of dynamic signals from ROIs
The included ROI Buddy software provides a graphical user interface (GUI) supporting the following functionality:
manual creation of ROIs
editing of ROIs resulting from automated segmentation
registration of ROIs across separate imaging sessions
Installation and Use
For complete documentation go to <http://www.losonczylab.org/sima>
Dependencies
Python 2.7
numpy >= 1.6.2
scipy >= 0.13.0
scikit-image >= 0.9.3
scikit-learn >= 0.11
shapely >= 1.2.14 (Windows users: be sure to install from Christophe Gohlke’s built wheels)
pillow >= 2.6.1
future >= 0.14
Optional dependencies
OpenCV >= 2.4.8, required for segmentation, registration of ROIs across multiple datasets, and the ROI Buddy GUI
picos >= 1.0.2, required for spike inference (>= 1.1 required for Python 3)
pyfftw, allows faster performance of some motion correction methods when installed together with FFTW.
h5py >= 2.2.1 (2.3.1 recommended), required for HDF5 file format
bottleneck >=0.8, for faster calculations
matplotlib >= 1.2.1, for saving extraction summary plots
mdp, required for ICA demixing of channels
If you build the package from source, you may also need:
If you are using the spike inference feature, we strongly recommend installing MOSEK (free for academic use) which greatly speeds up the inference.
Citing SIMA
If you use SIMA for your research, please cite the following paper in any resulting publications:
License
Unless otherwise specified in individual files, all code is
Copyright (C) 2014 The Trustees of Columbia University in the City of New York.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
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