[ome-devel] WellSample LSID (Cellomics )

[Jäälinoja Harri]

Hi Josh,


On 24/02/17 11:45, Josh Moore wrote:
>> I'm looking at
>> https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/CellomicsReader.java
>>
>> and wondering where in the OMERO database can I find the info that is store here:
>>
>> MetadataStore store = makeFilterMetadata();
>> ...
>>        int fieldIndex = getField(file);
>> ...
>>          String wellSampleID =
>>            MetadataTools.createLSID("WellSample", 0, wellIndex, fieldIndex);
>>          store.setWellSampleID(wellSampleID, 0, wellCntr, fieldCntr);
> The column `well_index` on `wellsample` contains this information.
> This doesn't show up in the Hibernate object, but instead is the
> position of the wellSample in the list Well.wellSamples.
I looked, but it doesn't look like the original numbers are there.

omero=> select id,well_index,image,plateacquisition from wellsample 
where well_index > 100;
  id | well_index | image | plateacquisition
----+------------+-------+------------------
(0 rows)

I just imported a plate like this:

hajaalin at dhcp-asv-66:/mnt/lmu-archive/LMU-archive2/users/FROM_CELLINSIGHT/LMU-CELLINSIGHT_140628160001$ 
ls *A01*| sed -e 's/f/f /' -e 's/d/ d/'|sort -n -t' ' -k2 |head -2
LMU-CELLINSIGHT_140628160001_A01f 67 d0.C01
LMU-CELLINSIGHT_140628160001_A01f 67 d1.C01
hajaalin at dhcp-asv-66:/mnt/lmu-archive/LMU-archive2/users/FROM_CELLINSIGHT/LMU-CELLINSIGHT_140628160001$ 
ls *A01*| sed -e 's/f/f /' -e 's/d/ d/'|sort -n -t' ' -k2 |tail -2
LMU-CELLINSIGHT_140628160001_A01f 126 d0.C01
LMU-CELLINSIGHT_140628160001_A01f 126 d1.C01

So there should be a well_index of 126, but the maximum is 59. I 
understood from an example Ola sent earlier that the Hibernate object 
wouldn't have it, but it's strange that it's not in the db either. The 
CellomicsReader code looked to me like it would store the original id.

>> The point is that fieldIndex is read from the filename, and may be different than fieldCntr. For example if the fields are collected in a spiral pattern that does not start in the center, the first fieldIndex may be e.g. 50. OMERO plate viewer shows fieldCntr (or some index starting at 1). If I want to find individual original files that contributed to a field, I need to find this mapping from fieldCntr to the original field index.
> You can also attempt to use omero.cmd.UsedFilesRequest:
>
> https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/blitz/resources/omero/cmd/FS.ice#L85
>
> which will give you a list of files that match the particular series.
> You can see an example of its usage here:
>
> https://github.com/mtbc/omero-downloader/blob/dev_5_3/src/main/java/org/openmicroscopy/client/downloader/Download.java#L239
I didn't try this yet, but I suspect that if UsedFiles is same as 
Fileset.usedFiles, the problem will be that when a screen is uploaded, 
each of the displayed images refers to the entire set, not only the 
channels of a particular field.

It's tempting to try to find the filenames, because I'd be able to 
process the data without transferring them. But then again, these are 
not huge datasets, so probably transferring is not a problem. I'll try 
that approach (CellProfiler data lists with omero iids) next.

Thanks, and have a good weekend!
Harri

>
>> Thanks, best regards,
>> Harri
> All the best,
> ~Josh
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