Review and update spatial sections

[brianraymor]

5.3.0: Visium Spatial Gene Expression ("EFO:0010961") is now a parent term introduced by [NTR] Version specific Visium assays. CELLxGENE Discover supports descendants of Visium Spatial Gene Expression.

CELLxGENE Discover currently only contains Visium Spatial Gene Expression V1 datasets, so the required change would be to update the references from Visium Spatial Gene Expression to Visium Spatial Gene Expression V1. The following assays do not need to be supported at this time:

• Visium CytAssist Spatial Gene Expression V2: Visium CytAssist
• Visium CytAssist Spatial Gene Expression, 6.5mm: Visium CytAssist, 6.5mm
• Visium CytAssist Spatial Gene Expression, 11mm: Visium CytAssist, 11mm

Addressed in #1412

Review @jychien's related comments:

#1409 (comment)

Might be a misnomer to call the hires image a high resolution image. It is actually a downsampled image that is called hires, only because it is higher than the lowres image. It is the full res image that is the highest resolution: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs#tissue-png

Also, this section, in general, makes it sound like there should be images for Slide-seq. The CxG schema does not have images for Slide-seq.

#1409 (comment)

Sorry, I don't know how to comment on the array_col, array_row, and in_tissue tab. These obs fields are only applicable for Visium datasets.

[brianraymor]

@jychien @ivirshup

#1409 (comment)
Also, this section, in general, makes it sound like there should be images for Slide-seq. The CxG schema does not have images for Slide-seq.

I see the problem in the spatial section summary of requirements:

• Spatial Scenes with spatial data – census_obj["census_spatial_sequencing"][organism].spatial[scene_id] – SOMAScene. There will be as many Spatial Scenes as spatial datasets. EachSOMAScene MUST contain the following:
  • Positions array – census_obj["census_spatial_sequencing"][organism].spatial[scene_id].obsl["loc"] – SOMAPointCloudDataFrame.
  • High resolution image – census_obj["census_spatial_sequencing"][organism].spatial[scene_id].img[library_id]["highres_image"] – MultiscaleImage.

with a subsequent clarification of the requirement later in the schema:

Images of a Scene - census_obj["census_spatial_sequencing"][organism].spatial[scene_soma_joinid].img[library_id] – Collection of MultiscaleImage

Images of a Visium Spatial Gene Expression ("EFO:0010961") scene MUST adhere to the following specifications. Other assays MUST NOT have images, and MUST NOT include the img collection.

---

My sense is that part of the problem is the style of the census where requirements are summarized and then developed further in additional sections which results in duplication and/or misalignment of requirements. My objective would be to state the requirement once. I need to think about this from a structural perspective.

None of this is blocking for @mlin - I plan to submit a PR to only update all references from Visium Spatial Gene Expression ("EFO:0010961") to Visium Spatial Gene Expression V1 ("EFO:0022857"). The other tasks in this issue will require more editorial time.

[brianraymor]

Reminder: Add similar guidance:

Non-spatial data for organisms MUST be stored as a SOMAExperiment in census_obj["census_data"][organism] where the value of organism matches an organism defined in Census table of organisms – census_obj["census_info"]["organisms"] – SOMADataframe.

Addressed in #1412