Software for openscope
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sequence
README
README~
openscope_software.py
openscope_software.py~
test.jpg

README

Title: OpenScope Software Package
Date Started: 2012 Mar
Last Modified: 2012 Mar
http://www.asymptoticdesign.org/
This work is licensed under a Creative Commons 3.0 License.
(Attribution - NonCommerical - ShareAlike)
http://www.creativecommons.org/licenses/by-nc-sa/3.0/

In summary, you are free to copy, distribute, edit, and remix the work.
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===Description===
OpenScope Software Package is a package of python-based utilites meant to assist in common imaging tasks related to biological microscopy.  Currently the package is menat for fluorescence imaging.

===Usage===
Right now openscope-software has two modes: single and sequential analysis

python openscope-software.py [filename]
This will upload the file with a given filename into the Tkinter canvas.  Control-Clicking defines the corner of a rectangle; after two clicks a rectangle is drawn and the averaged intensity in the rectangle is printed to the standard output.

python openscope-software.py [fileroot] [extension]
This set of arguments runs openscope-software in sequential mode.  The software will look for all files in the directory with a given root filename and extension (e.g. 'test' and 'jpg' returns all files of the format test*.jpg), and then sorts them numerically.  The sequences of images should be numbered (image01.jpg, image02,jpg, image03.jpg,etc.).  The user can then control-click to define regions of interest in the image; control-spacebar brings up the next frame, recalculates the intensities in the same region, and writes them to file.  This is meant for tracking fluorescent dyes such as in Calcium Imaging.

===Dependencies===
Python 2.6
Python Imaging Library (+ python-imaging-tk)
TKinter