Software for analysis of sequential imaging data
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>
- 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
If you use SIMA for your research, please cite the following paper in any resulting publications:
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/>.
Release history Release notifications
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|Filename, size & hash SHA256 hash help||File type||Python version||Upload date|
|sima-0.2.1-cp27-none-macosx_10_9_x86_64.whl (2.5 MB) Copy SHA256 hash SHA256||Wheel||cp27||Aug 20, 2014|
|sima-0.2.1-cp27-none-win32.whl (2.3 MB) Copy SHA256 hash SHA256||Wheel||2.7||Aug 20, 2014|
|sima-0.2.1.linux-x86_64.tar.gz (2.7 MB) Copy SHA256 hash SHA256||Dumb Binary||2.7||Aug 19, 2014|
|sima-0.2.1-py2.7-linux-x86_64.egg (2.7 MB) Copy SHA256 hash SHA256||Egg||2.7||Aug 19, 2014|
|sima-0.2.1-py2.7-macosx-10.9-x86_64.egg (2.7 MB) Copy SHA256 hash SHA256||Egg||2.7||Aug 20, 2014|
|sima-0.2.1-py2.7-win32.egg (2.5 MB) Copy SHA256 hash SHA256||Egg||2.7||Aug 20, 2014|
|sima-0.2.1.tar.gz (2.5 MB) Copy SHA256 hash SHA256||Source||None||Aug 19, 2014|
|sima-0.2.1.win32-py2.7.exe (2.5 MB) Copy SHA256 hash SHA256||Windows Installer||2.7||Aug 19, 2014|
|sima-0.2.1.zip (2.6 MB) Copy SHA256 hash SHA256||Source||None||Aug 19, 2014|