README
------

CellOrganizer
For generating 3D images, using a computer with at least 2 GB of memory is recommended.

I. Installation
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To install CellOrganizer

(1) Download the latest distribution from

http://CellOrganizer.org/Downloads
or
http://murphylab.web.cmu.edu/software/CellOrganizer

(2) Unzip the distribution into a folder of your choice

(3) Start Matlab and change the default directory to the folder chosen above

II. Using CellOrganizer via the Graphical User Interface

Enter "startup" at the Matlab command prompt

III. Using CellOrganizer from the Matlab command line

Enter "startup" at the Matlab command prompt to add the relevant paths.  The main CellOrganizer commands are

> img2slml

which trains a model from a set of images

and

> slml2img

which synthesizes one or more image(s) from a trained model.

IV. Examples using the Matlab command line

There are a numbers of demo files that illustrate how to use CellOrganizer from the command line.  Type

> demoinfo

to get a listing of available demos.

