SLAP2 metadata requirements

[dbirman]

Notes from discussion with Kaspar on 5/8:

• Slap2 scope generates its own metadata files, we should continue to store these in data assets
• Slap2 team will be responsible for maintaining an instrument.json file and updating it when changes occur, these are timestamped during microscope startup
• A lot of on-prem analysis happens to do ROI extraction etc after an acquisition. Once this is done we want to insert a mapper that pulls the acquisition.json out of the Slap2 metadata json. At this time we will run the mapper-cli as well to get the data_description, subject, and procedures

Requirements:

• We want to be able to search easily over Slap2 microscope modes (raster, etc) as well as ROI types
• We want to be able to search easily over "is simple raster" field
• These two fields ^ should probably go in the Slap2MicroscopeConfig
• Channel/Plane information are all available in the metadata files and can be pulled out
• We won't bother pulling out parse plan, dilation, etc, which will still be available in the generated metadata file anyways
• There are in general two kinds of image coordinate systems, both of which need to be re-calculated after the fact: either a low-res FOV image is taken that allows for image alignment, or the stage is calibrated so that a (0,0,0) origin is at a known coordinate and then the relative position of the stage is recorded. We should support both kinds of coordinate systems in some way.
• Intended measurement field should be expanded to allow for lists from a controlled vocabulary of options (things like "broad tufted", "layer 2", etc). This list needs to be limited for Slap2 but expandable. One option is to embed this in the mapper?
• Mapper should handle gathering the FOV image and storing it's AssetPath information in the metadata

[dbirman]

Follow-up plan:

• We'll jointly upgrade the existing rig.json to a 2.0 instrument.json (using office hours time)
• Dan or someone else will implement the metadata mapper to convert the current metadata json format into an acquisition json

[dougollerenshaw]

@saskiad and @dbirman discussing intended_measurement during triage. Saskia arguing that structures (eg "broad tufted") does not belong here.

Need another field to contain this. Requires more conversation.

[dbirman]

@dbirman todo for myself: remove dilation before 2.0 goes live

[dbirman]

@dbirman Write the mapper so that we can actually start iterating on this

[dbirman]

Notes from Michael

• DMD should be a deviceconfig in Slap2Channel
• Dilation in Slap2Channel
• Power may need to move because the HWP/DMD modify the power in the light path
• SlapPlane will have targeted_neuron / targeted_branch (?), branch should probably go away
• sampling_strategy needs to move into Slap2Channel because the DMD is part of the channel and controls the per-pixel framerate

[dbirman]

Changes made following on meeting with Arielle/Michael