Software for openscope
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Failed to load latest commit information.


Title: OpenScope Software Package
Date Started: 2012 Mar
Last Modified: 2012 Mar
This work is licensed under a Creative Commons 3.0 License.
(Attribution - NonCommerical - ShareAlike)

In summary, you are free to copy, distribute, edit, and remix the work.
Under the conditions that you attribute the work to the author, it is for
noncommercial purposes, and if you build upon this work or otherwise alter
it, you may only distribute the resulting work under this license.

Of course, these permissions may be waived with permission from the author.

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.

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

python [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 [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.

Python 2.6
Python Imaging Library (+ python-imaging-tk)