Software for analysis of sequential imaging data
The SIMA (Sequential IMage Analysis) package facilitates 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:
- 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>
- Python 2.7
- numpy >= 1.6.2
- scipy >= 0.13.0
- matplotlib >= 1.2.1
- scikit-image >= 0.9.3
- shapely >= 1.2.14
- OpenCV 2.4 (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
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-0.2.0-py2.7-linux-x86_64.egg (2.7 MB) Copy SHA256 hash SHA256||Egg||2.7||Aug 18, 2014|
|sima-0.2.0.tar.gz (2.5 MB) Copy SHA256 hash SHA256||Source||None||Aug 18, 2014|
|sima-0.2.0.win32-py2.7.exe (2.6 MB) Copy SHA256 hash SHA256||Windows Installer||2.7||Aug 18, 2014|
|sima-0.2.0.win-amd64-py2.7.exe (2.6 MB) Copy SHA256 hash SHA256||Windows Installer||2.7||Aug 18, 2014|
|sima-0.2.0.zip (2.6 MB) Copy SHA256 hash SHA256||Source||None||Aug 18, 2014|