Multiple fields per well

[dsudar]

Following up on the discussion started on: https://forum.image.sc/t/omero-parade-accepting-stringcolumns-from-omero-metadata-and-loading-multiple-plates/27767/16 on how to deal with multiple fields/images per well, I'd like to offer some suggestions:

1. on @will-moore 's concern how to how handle the Plate view display, I think the current approach of just showing the first field in the well is adequate since the Plate view is likely only used in the filtering step when Well level experimental metadata is used to filter down to the conditions of interest. Maybe put up a warning that only field 1 per well is shown. To make it more "cute", it would be fun to use the "Field positions in well" panel to show per field heatmap detail when the user selects a single well while in heatmap mode.
2. Most of the measured values that one would want to display are typically reported per field and not per well. So indeed, the Table/List view and Scatter Plot view should show the fields/images. And consequently the bulkannotations tables should be attached to Field/Image rather than to Well as currently. To make that convenient, it would be nice to provide an update to Populate_Metadata.py and its underlying code to easily do so.
3. The above will also resolve an issue with displaying whatever image data is selected using the Scatter Plot or Table/List: currently such a selection is a list of wells which iviewer does NOT accept; if such a selection is a list of images, then iviewer can accept that as a multi-selected set and provide great visualization of that set.

Thanks for considering,
Damir

[will-moore]

Hi Damir,
I've been exploring ways to handle data on multiple Fields vv Wells. This is a demo of a prototype where I'm handling data for ROIs in Plates with multiple Fields per Well.
The Screen/Plate/Well part of the demo starts at https://youtu.be/FyjGhZxx6es?t=534
The code is at https://gitlab.com/openmicroscopy/incubator/parade-crossfilter.
This demo video only shows 3 or 5 Fields per Well, so I'm not sure if that approach would work for larger numbers, but I'd be interested to get your impression?
And if you'd like to try it out, it shouldn't be too hard to install and build (similar to current OMERO.parade).
Thanks,
Will

[abhamacher]

Hi Damir, hi Will,

to put it into the right repo and to update the current situation regarding this issue, I would like to add something already mentioned at the omero-metadata repo (ome/omero-metadata#64).

1. When populating image-based data with omero-metadata, OMERO.parade can properly load individual image data for example in the filter menu (see Example 68...366 per image) but the dots in the parade plot do still not cover all images, but rather wells only, which is inconsistent.

(as a side note, with the same OMERO.table plots in parade-crossfilter show all individual image dots)

2. Based on issue no. 1, using OMERO.parade one cannot see if the data shown is coming from wells or from images. Typically someone would populate the OMERO.table but another or multiple persons would browse through the data, which are not aware of the underlying data structure. So this is something that should be visible somehow to the user.

3. These two issue also apply to roi-based data.

Even if OMERO.parade is not able to handle multiple images per well or even ROIs, it should be at least consistent and allow some kind of data source transparency to the users to avoid misinterpretation of the presented data.

Maybe put up a warning that only field 1 per well is shown. To make it more "cute", it would be fun to use the "Field positions in well" panel to show per field heatmap detail when the user selects a single well while in heatmap mode.

This sounds nice to me too, by the way.

Thanks,
Anna