openmicroscopy/openmicroscopy — pull request #1302 by will-moore (2013-06-17 15:00:57+00:00)
Title: Python code examples and scripts for Paris

Some new / moved examples:

- A simple FRAP script (standalone)
- A Transform_Image OMERO.script to rotate or flip an image
- An example of using ImageJ to process images
- Shapes_To_Table.py has also been moved into the new OMERO.scripts dir

To test - bit tricky.
FRAP needs an example FRAP image that I have, with an ROI ellipse drawn on the bleach spot, extending across all time points. Check that you get reasonable values of tHalf (2 secs in my example) and mobile fraction (0.6 approx) and open the FRAP.csv that is produced in Excell to view the curve plot.

Transform_Image is pretty straight-forward. Simply run this on any non-big image and choose one or more transforms to perform (rotate, flip etc). Check you get a new image that corresponds to these transforms.

Transform_Image requires that you have ImageJ installed on the server and that the ImageJ path in the script points to the imageJ .jar. Then you need to run the script on a Z-stack image (not too big) and check you get a "Rotation Projection" new image in OMERO.

Shapes_To_Table has simply been moved. Doesn't really need testing.