Create Montages and/or Overlays in MetaXpress version 6
File Name: Create Montages and Overlays_revA.jzp

This journal creates montage images, overlay montages , and/or overlay images of individual sites, automatically across a plate.  This journal has the following features:
• Option to have the  journal automatically calculate the rows and columns 
• Automatically fills in gaps in the site layout
• Option to have the journal automatically calculate site overlap based on stage positions
• Choose between stitching or cropping when there is site overlap
• Option to automatically detect the individual wavelengths on a plate and montage all of them in one run
• Automatically creates a separate folder for each plate
• Automatically saves individual wavelength montages in HTD format for simple import back into the database
• Overlays can use up to 6 colors: Gray, Red, Green, Blue, Yellow, Cyan
• Option to create different combinations of overlay colors
• Option to specify the final zoom of the image, with automatic reduction of the zoom if the expected montage exceeds software limits
• Saves user-defined settings, so that the interactive setup does not need to be repeated to rerun the same assay
• Handles user selection of multiple time points or Z steps
• For advanced users, the option to add an analysis routine to be performed on the montages, with the choice to enable or disable saving of the montages
• For advanced users, the option to add graphics (such as a scale bar/calibration bar) to overlay images

• MetaXpress 6 or above (images acquired in an earlier version are OK)
• Recommended to use images that have been acquired with an ImageXpress Micro or Ultra system
• Images that have been imported from another microscope can be processed,  but some features may not be available

• Images must be available through the database (e.g. via Review Plate Data)
• Consider enabling disk swapping in Edit > Preferences > Stack Buffering

See detailed notes in the attached document, located in the .zip file.  The PDF was too large to attach without compressing it.
The .jzp file contains the actual journal files.

Attached Files
.jzp   Create Montages and Overlays_revA.jzp (Size: 114.79 KB / Downloads: 81)
.zip   Create Montages and (Size: 2.28 MB / Downloads: 62)
If you are experiencing errors when running this journal, please recheck settings.  I will add more error handling in the next version.  If it does not seem to be related to settings, try exiting and restarting MetaXpress to see if that resolves the error.  

Some settings that have caused errors for users:
- Running on a plate with 1 site/well.
- Using the option for specified wavelengths and the wavelengths do not match those available for the current plate (settings were created with a different plate).
- Using the image file server location as the parent directory for saving the montages.  It is safer to save to a separate location.
- Parent directory is not available or writable from the current computer (settings were created on a different computer).
The automatic calculation of rows and columns may fail if there is no image for the upper left site position.
for example, a well layout like this:


In this case, use the option to specify the number of rows and columns.
The example above would be 5 rows and 5 columns.

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