MORPHEUS for Fiji Files

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MORPHEUS' quick start guide
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morphversion 1.0/2019
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MORPHEUS plugin can be easily integrated into Fiji menu, simply by copying Morpheus_.ijm file into the Fiji's plugins subfolder.

Once installed, the user can launch MORPHEUS from the Plugins menu and MORPHEUS main window should appear.

Through this dialog window, it is possible to specify the following parameters:
 - the path of the input directory (i.e. the folder containing the images to be analyzed);
 - the path of the output directory (i.e. the folder in which MORPHEUS will save the results of the analysis);
 - image file suffix (i.e. the extension of the images to be analyzed);
 - nucleus file identifier (i.e. a string of characters that must be present in the file name of all the images stained for nucleus, but NOT in the images stained for cytoskeleton, allowing MORPHEUS to distinguish among them);
 - the anti-spot lower bound epsilon (i.e. the minimum number of pixels a segmented object must have to not be discarded as 'spot noise');
 - tolerance value T (i.e. the number of standard deviations from the mean of the sampling distributions used by MORPHEUS to define the characteristic area and circularity of the 'typical' isolated cell. The higher the value of T, the more tolerant the selection process will be);
 - 4 checkboxes that allow the user to choose which MORPHEUS' optional functions to enable among Orientation analysis, Nucleus analysis, Full output and Verbose log.

NOTE: Orientation analysis requires OrientationJ plugin (version 2.0.2 or above) to be installed.
OrientationJ latest version can be freely downloaded at http://bigwww.epfl.ch/demo/orientation/.

When clicking OK button, MORPHEUS starts scanning the user-defined input folder searching for the images stained for cytoskeleton and no further intervention by the user is required until the analysis of the whole dataset is completed.

In any case, after MORPHEUS terminates, it is always recommended to check the results of both segmentation and cell detection processes.
Badly thresholded images can be easily spotted by a quick visual inspection of the output folder content and their possible presence usually indicates an insufficient image quality.

If everything worked properly, the message 'All output files have been correctly saved to <output>' is printed in Fiji Log window.

For a more detailed guide to MORPHEUS algorithm and output, please refer to 'MORPHEUS - User Guide and SM.pdf'.