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sima 0.2.0

Software for analysis of sequential imaging data

Latest Version: 1.3.2


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 <>


  • 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


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 <>.

File Type Py Version Uploaded on Size
sima-0.2.0-py2.7-linux-x86_64.egg (md5) Python Egg 2.7 2014-08-18 2MB
sima-0.2.0.tar.gz (md5) Source 2014-08-18 2MB (md5) MS Windows installer 2.7 2014-08-18 2MB
sima-0.2.0.win32-py2.7.exe (md5) MS Windows installer 2.7 2014-08-18 2MB (md5) Source 2014-08-18 2MB