ImageJ plugin - channels

jburel commented 5 years ago

When adding the "Split channels" option to the Crop workflow in ImageJ, see for example Fiji section, crop workflow of https://downloads.openmicroscopy.org/presentations/2019/Dundee-April/Dundee_April_2019_Day2.pdf

The channels names are not preserved correctly when the crop is imported back to OMERO.

lets have an image in OMERO with channels A, B, C
lets use the insight-ij plugin to open this image in Fiji and when in B-F dialog
lets select the "Split channels" checkbox
in Fiji, draw a rectangle on the image from channel C, then Image > Crop
Select Plugins > OMERO > Save image to OMERO and import the cropped image
in OMERO, observe that the crop is having one channel only (expected), but the name of this channels is "A" (not expected, "C" should be the name)

jburel commented 4 years ago

see https://github.com/ome/omero-insight/pull/122

jburel commented 4 years ago

The first part of the problem has been fixed in #122. We use the title of the ImagePlus as the name of the image The second part of the issue is a problem with the BioFormats export plugin. cc @dgault

ome / omero-insight

ImageJ plugin - channels #48