How to handle 60+ unstitched tiles for a single CODEX Assay?

[mccalluc]

User story
The CODEX data will be unstitched, so for each details page, there with be 60+ images, each covering a separate region, each with 2000+ cells. Having 60 image panes will not work.

Proposed solution
Right now, the CELLS_ADD / CLUSTERS_ADD / etc. events are only published by the invisible LayerPublisher component on load... but it doesn't seem unreasonable to have a visible component the user could interact with which would publish *_ADD events.

(I'm not sure right now what would happen if a component received an ADD after it has already been initialized. The name of the event is not quite right: We are actually adding and replacing, but ADD is concise, and clear enough for now.)

As far as UI, I think the radiobutton idiom we already have could be extended, so it would be something like:

◉ Row 1, Column 1
◎ Row 1, Column 2
◎ Row 1, Column 3
◎ Row 2, Column 1
...

---

@ngehlenborg / @ilan-gold / @manzt : Please review, and add a comment below or let me know in person what you think of this.

[manzt]

I think this is a good solution. We could think of other UI components to interact with the data described as well, (ie discrete slider for row and discrete slider for column).

[ngehlenborg]

Regarding the UI: while the above would work, I think we should move away from the radio button lists and replace them with tables that have a selection control (radio button or check box) because they afford sorting on different attributes (here: row, column) and searching across labels (very useful in the context of the gene list that we are currently using and I anticipate we will see many other scenarios in which that list gets quite long and where the entities in the list might have multiple attributes). I see that the downside of this approach is that we need to associate attributes (here: row, column) with the data sets (sub data sets?) that we load.

Regarding the data management: Would a selection view as described above be controlling all other views in the view configuration? In the context of CODEX I anticipate having views for:

• spatial data (i.e. images and overlaid segmented cells)
• channel mixing controller for the spatial view
• heatmap for antigen levels per cell (or other "abundance profile view" for selected cells)
• possibly other utility views such as a heatmap for the channel covariance matrix that Ted mentioned

Since each of these views is associated with one of the ~60 multi-channel images (i.e. tiles), each of them would need to update when a different tile is selected. Is that the plan?

[ngehlenborg]

Here is a graphical summary of what I described above:

(source: https://docs.google.com/presentation/d/1qwnhh5SY1lrdyc2mGcJuNYKvzKhqqKsURI61eQP5HsY/edit#slide=id.p)

[ngehlenborg]

Per discussion about CODEX/SPRM outputs (https://docs.google.com/presentation/d/1jRepy954XTmXrqiyneue1pdlUHgw1SIczNBwrz4aWTQ/edit#slide=id.g70e6c261c9_4_27): in addition to the X and Y, there can also be an R (region), which could be another column in the table described above.

[ilan-gold]

An option I had brought up a while ago in a conversation would be to use sliders for the xy positions of the tiles - I don't think the tile names are very important and this would save us from building a giant table with radio buttons and the like.

[ngehlenborg]

I spoke to @keller-mark and we agreed to discuss this issue (#489) in the team meeting on Friday. We need to address both UI and data management.

[mccalluc]

@ilan-gold : We got something up for the portal demo to handle the multiple tiles. I'll close this... but open a new focussed issue if you think there is still work to do? (Or reopen this if I'm confused about what work is already done.)