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Hi Etienne,
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<div class=""> If you have images already imported into OMERO, you can add them to a Well as in the Dataset_To_Plate script:</div>
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<div class=""><a href="https://github.com/ome/scripts/blob/develop/omero/util_scripts/Dataset_To_Plate.py#L57" class="">https://github.com/ome/scripts/blob/develop/omero/util_scripts/Dataset_To_Plate.py#L57</a></div>
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<div class="">However, if you have 2 images that are separate Channels, it sounds like you should be combining </div>
<div class="">these into a single 2-channel image in OMERO.</div>
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<div class="">I think one option could be to define a “pattern file” to specify how Bio-Formats should combine the images</div>
<div class="">on import.</div>
<div class=""><a href="https://docs.openmicroscopy.org/bio-formats/5.8.2/formats/pattern-file.html" class="">https://docs.openmicroscopy.org/bio-formats/5.8.2/formats/pattern-file.html</a></div>
<div class="">Although it’s possible you’d have to re-name the images to fit the pattern naming.</div>
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<div class="">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).</div>
<div class="">For example, if you can get a numpy array of each channel, you can create a new image in OMERO as in the</div>
<div class="">OMERO.figure, creating an image in OMERO from a single 3-channel PIL image (tiff_figure) </div>
<div class=""><a href="https://github.com/ome/omero-figure/blob/master/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py#L2030" class="">https://github.com/ome/omero-figure/blob/master/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py#L2030</a></div>
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<div class="">Hope that helps.</div>
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<div class=""> Will.</div>
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<div class="">On 11 Jun 2018, at 21:18, Etienne Dumoulin <<a href="mailto:etienne@phenomic.ai" class="">etienne@phenomic.ai</a>> wrote:</div>
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<div class="">Hi Omero developers,</div>
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<div class="">I have a new set of data that I cannot load directly into a screen using "omero import ... -r ...".</div>
<div class="">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.</div>
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<div class="">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?<br class="">
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<div class="">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.</div>
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<div class="">Thank you for your time.</div>
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<div class="">Etienne<br class="">
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<div class="">Etienne Dumoulin</div>
<div class="">PhenomicAI</div>
<div class="">Lead software engineer</div>
<div class="">+1 (416)-471-8323<br class="">
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