sima 0.3.1

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 (http://python.org)

• numpy >= 1.6.2 (http://www.scipy.org)

• scipy >= 0.13.0 (http://www.scipy.org)

• matplotlib >= 1.2.1 (http://matplotlib.org)

• scikit-image >= 0.9.3 (http://scikit-image.org)

• shapely >= 1.2.14 (https://pypi.python.org/pypi/Shapely)

Optional dependencies

• OpenCV >= 2.4.8 (http://opencv.org), required for segmentation, registration of ROIs across multiple datasets, and the ROI Buddy GUI

• h5py >= 2.3.1 (http://http://www.h5py.org), required for HDF5 file format

• pylibtiff (https://code.google.com/p/pylibtiff/), required for more efficient handling of large TIFF files

• mdp (http://mdp-toolkit.sourceforge.net), required for ICA demixing of channels

Citing SIMA

If you use SIMA for your research, please cite the following paper in any resulting publications:

Kaifosh P, Zaremba J, Danielson N, and Losonczy A. SIMA: Python software for analysis of dynamic fluorescence imaging data. Frontiers in Neuroinformatics. 2014 Aug 27; 8:77. doi: 10.3389/fninf.2014.00077.

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/>.