Scoping of Well-Field Grid View - Round 2

[gusferguson]

Following feedback and discussion on the first round of mockups: Scoping of Well-Field Grid View - Round 2 https://github.com/openmicroscopy/design/issues/49

Note: For convenience mockups show OMERO.insight only - exactly the same will be done in OMERO.web.

Agreement:

• look at various options for keeping plate view in centre pane when grid view opens using split pane - to allow:
  • context to be retained
  • easy movement from one well to another
• include a thumbnail grid in left hand pane to replace current red widget - acts like “birdseye” view

Some discussion about:

• having plate be above or below the grid
• thumbnails of all fields show in RHP when well is selected.

Run selected - no well selected

• shows “birdseye” view in LHP
• toolbar - field and grid view etc. elements greyed out
• Plate name added to Plate Run Details in RHP for consistency - this is included in Well and Field details
• annotations would be linked to Run

Well selected

• toolbar - field and grid view elements available
• need to add Run and Well into hierarchy in RHP
• no field/image details in RHP
• annotations would be linked to Well

Missing:

• ability to select all fields in single/multi-selected wells/all wells in a run - to annotate

Well - grid view selected

• toolbar - field and grid view elements available
• need to add Run and Well into hierarchy in RHP
• image details
• need to add Well name to Field Details in RHP for consistency
• annotations would be linked to field
• multi-selection and batch annotation possible

8 Fields in Well - Well overview at bottom

8 Fields in Well - Well overview at top

13 Fields in Well

• Well overview reduced in size when field no. increases
• scroll bars in plate overview

Zoom into Fields in grid view

• Well overview reduced in size
• scroll bars in grid view

Spatial view

• showing Fields in layout of physical location in 10x10 Well

Spatial view with Plate overview at top

Spatial view with “no image” icon in empty positions

Comments and feedback welcome.

[bramalingam]

Just a few comments on the design:

1) Just not sure about the value addition of the birds eye-view (Given the space it occupies): If its just for navigation purposes can it be part of the centre panel itself (like big images).

• Can that space be use for : Thumbnail spatial view of the fields within a well (normalising the size of the thumbnails to the area covered within a well) would be a good value addition. And will give context to the users in terms of the position of the different fields within the well, and the fraction of area acquired within the well.

2) Multi-Selection cases: If I want to compare controls from 6 different positions within a plate: say B6, F8, G9, A10,....

• There is no easy way (currently) to navigate and compare all fields within these wells together. A multi selection view could work similarly to the well-overview, with wellIds on the Y axis, and the field numbers on the x axis (i.e, another grid view in the field-overview section). This would help me create a fractional plate view, which was something that was useful during the QC process (at NCBS, India).

[jburel]

if we have the "plate view" under the grid view, we should remove the "red-grid"

[will-moore]

Seems my comment https://github.com/openmicroscopy/design/issues/49#issuecomment-239185563 got a bit lost at the end of Round 1. Adding some more screenshots and details here:

Run Selected

Well Selected At the bottom of the centre panel we show the first few images from the Well alongside a "Show All" button. This is like a "Preview" of the Images in a Well. You may wish to preview a bunch of Wells before you want to see all the images in a chosen Well. This makes it clear that each Well does contain more images, which may not be so obvious otherwise (particularly if you are viewing data that you're not familiar with E.g. IDR. It also makes it clear how to see all the images in a "Grid view" whereas this may not be so obvious otherwise.

Grid View Having clicked "Show All" you now see all the images for the selected well. The Plate view (above) is reduced in size (zoomed out) BUT the user can zoom the Plate or the Images and adjust the divider between them depending on how much detail they wish to see from each. E.g. Plate view may still provide some indication of which Wells are interesting. NB: Although the thumbnails for each Well in the Plate are just the first field, this could be improved E.g. mosaic of all fields OR user-chosen field. In "Grid View" you can restrict the number of Images per row.

Image Selected With a Well selected (with or without Grid view) you can click a thumbnail to load that Image in the right panel.

Putting it all together:

[gusferguson]

@will-moore - thanks for all the mockups. Your comment in Round 1 wasn't overlooked, I was just starting with new points arising from discussions that hadn't been mockup-up at all.

[gusferguson]

Points after discussion with @bramalingam

• "no-image" icon on spatial view unnecessary clutter
• would be useful to have multi-selection of wells in top well view with each well in a row in section below - then can multi-select wells and use horizontal and vertical scroll to compare zoomed in views of fields (in columns) - see mockups below:
  • 1 (wells selected)
  • 2 (individual field selected)

.

• have spatial view of well in LHP instead of red widget
• have red widget as equivalent of Big Image birds-eye in centre pane - would allow quick navigation around plate - see mockups below:
  • 1 - birds-eye in well section of CP (preferred)
  • 2 - in bottom right corner.

[jburel]

• For spatial view you will need axis and units so people have an idea where fields are physically
• Red grid will be useful when we cannot view the full plate. We will probably need a way to minimize it, similar to bird-eye view

[gusferguson]

@jburel - can you give me example of how axis and units could be displayed - not shown on current spatial view.

[gusferguson]

Comments from @jburel :

• spatial view likely to be too large to be practically shown in LHP
• layout of fields in spatial view usually scattered - not a neat grid

[jburel]

We could display in LHP if the grid is very small and the "thumbnail/black dots" indicate where the fields are. "Thumbnails" cannot be used for visualisation. The position needs to be indicated in tooltip.