Overview
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>
Dependencies
Python 2.7
numpy >= 1.6.2
scipy >= 0.13.0
matplotlib >= 1.2.1
scikit-image >= 0.9.3
shapely >= 1.2.14
Optional dependencies
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
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/>.
3 maintainers
Metadata
3 maintainers
Release files for sima 0.2.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distributions (sdists)
| File | Size | Uploaded | |
|---|---|---|---|
| sima-0.2.0.zip | 2.6 MB | Details | |
| sima-0.2.0.tar.gz | 2.5 MB | Details |
Built distributions (wheels)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| sima-0.2.0.win-amd64-py2.7.exe | Details | |||
| sima-0.2.0.win32-py2.7.exe | Details | |||
| sima-0.2.0-py2.7-linux-x86_64.egg | Legacy Egg format | - | - | Details |
Total release size: 13.0 MB
Release files / sima-0.2.0.zip
| Download URL | sima-0.2.0.zip |
|---|---|
| Size | 2.6 MB |
| Tags | Source |
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Release files / sima-0.2.0.tar.gz
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| Size | 2.5 MB |
| Tags | Source |
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Release files / sima-0.2.0.win-amd64-py2.7.exe
| Download URL | sima-0.2.0.win-amd64-py2.7.exe |
|---|---|
| Size | 2.6 MB |
| Tags | Source |
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Release files / sima-0.2.0.win32-py2.7.exe
| Download URL | sima-0.2.0.win32-py2.7.exe |
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| Size | 2.6 MB |
| Tags | Source |
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Release files / sima-0.2.0-py2.7-linux-x86_64.egg
| Download URL | sima-0.2.0-py2.7-linux-x86_64.egg |
|---|---|
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