Implement QC Capsule

[alexpiet]

Is there data? (NAN, number of frames)
if <1200frames (=1min), likely a test sessions or alike
Are there NaNs in either the raw FIP data or processed FIP data?

number of ROI (columnN of the CSV) correct?
checking the source CSV (maybe QA) and nwb packaged data

Some metric of SNR.
histgram of raw values to see baseline intensity, fluctuations

Is there saturation ?
if == 65535 (16bit)

Is the trace stable?
histgram of 1st derivative, outlier detection (>% of sliding baseline mean, etc)

Are there dropped frames?
number of frames for 3 ch the same? same as number of sync pulses? (but can be QA-level)

Is there cross-talk between channels?
correlations between fibers/channels but can be tricky as we may be actually measuring highly correlated signals.

Is there bleaching?
histogram of subtracted bleaching?

Is there timing issues? Different channels locked to one another properly.
TBD what would be the best (should be agnostic to specific behavior)

[alexpiet]

• link to QC examples
• need to specific what the QC capsule should do
  • Read data
  • create evaluate object
  • create metrics
  • store outputs in docdb

[jeromelecoq]

Ok. So first, you best source of information on this is @dbirman

Here are some useful instructions.
https://aind-data-schema.readthedocs.io/en/latest/quality_control.html

Here is an example QC capsule template : https://github.com/AllenNeuralDynamics/aind-qc-capsule-example/blob/main/code/run_capsule.py

Here is the QC portal that is pulling those metrics real-time (4h delay currently). https://qc.allenneuraldynamics.org/qc_portal_app

[jeromelecoq]

I would recommend you both block one or 2 afternoon of work to get this started.

[rachelstephlee]

Kenta is still working on this.

By the end of the year, Dan and Kenta will put together a design.

By next year, Dan will help out Kenta to do this.

Jerome said that higher order analysis will be higher priority next year, so the sooner we can wrap this up, the better it will be.

[rachelstephlee]

@dyf says it should be trivial to add an additional QC (but if we want to update backwards it will take more work).

Jerome thinks success for EOY is:

• Data collected, processed, tracked, and QC within 24 hours.