sima 1.3.1

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

• 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:

• Cython

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:

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/>.