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Task #10648 (new)

Opened 11 years ago

Last modified 8 years ago

Command-line processing via Scripts Example

Reported by: wmoore Owned by: wmoore
Priority: major Milestone: Unscheduled
Component: Scripting Version: n.a.
Keywords: n.a. Cc: rleigh
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.


Need to provide an up-to-date example of processing via command line called from Scripting service". We could use ImageJ as an example, since we know this is useful.

See: https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=4650
And: https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=3082

Ideally this would take a Tiff stack (or a single Tiff) and generate a processed Tiff stack (or single Tiff).

Most of what we need is in this example (we write a macro and pass it to ImageJ along with a tiff stack), https://github.com/will-moore/weblabs/blob/master/views.py#L74 except that it is in the web framework and it only generates a jpeg output (not suitable to upload back to OMERO as a new image).

First task is to identify a suitable macro / process to call on the command line from ImageJ, otherwise I'll just go with the example we have and upload jpegs as new images.

Change History (1)

comment:1 Changed 8 years ago by jamoore

  • Milestone changed from 5.x to Unscheduled
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