[ome-devel] Importing Images in a new Screen Manually

[William Moore (Staff)]

Hi Etienne,

 If you have images already imported into OMERO, you can add them to a Well as in the Dataset_To_Plate script:

https://github.com/ome/scripts/blob/develop/omero/util_scripts/Dataset_To_Plate.py#L57

However, if you have 2 images that are separate Channels, it sounds like you should be combining
these into a single 2-channel image in OMERO.

I think one option could be to define a “pattern file” to specify how Bio-Formats should combine the images
on import.
https://docs.openmicroscopy.org/bio-formats/5.8.2/formats/pattern-file.html
Although it’s possible you’d have to re-name the images to fit the pattern naming.

An alternative might be to manually create a new Image in OMERO via the Python API, if you can open the images in Pillow (e.g. TIFF, png etc).
For example, if you can get a numpy array of each channel, you can create a new image in OMERO as in the
OMERO.figure, creating an image in OMERO from a single 3-channel PIL image (tiff_figure)
https://github.com/ome/omero-figure/blob/master/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py#L2030

Hope that helps.

  Will.



On 11 Jun 2018, at 21:18, Etienne Dumoulin <etienne at phenomic.ai<mailto:etienne at phenomic.ai>> wrote:

Hi Omero developers,

I have a new set of data that I cannot load directly into a screen using "omero import ... -r ...".
I think it makes sense because the folder does not contain any bio-format xml metadata. Therefore, I need to load it manually using a file name regular expression.

I have found a way of creating a new plate, well, well sample and link them together. However, I am not sure how to link my two images (I have two channels) to a well sample. Could you let me know where this is stored in the database or/and the relevant Python wrapper classes?

Overall, I feel I am probably not the only one with this type of use case, but I did not find any relevant documentation on this, so please let me know if I overlooked something and there is an easier way.

Thank you for your time.

Etienne

--
Etienne Dumoulin
PhenomicAI
Lead software engineer
+1 (416)-471-8323
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