Neurophotometrics FP3002 - Extract data from a single ROI?

[Søren HJ]

Hi  Gonçalo 

I am in the process of switching from the old Neurophotometrics fiber photometry system FP3001 - to the new FP3002 system.

I am wondering if there is a way to extract/visualize the photometry data from individual ROIs (0G, 1R, 2G, 3R etc.) live in bonsai, preferably with a y-axis? 

Currently, data from all assigned ROIs are displayed simultaneously in the same visualizer (for the L470 node for example) - but I like to inspect the individual signals more thoroughly before starting an experiment, to check that I am getting a correct signal, and it gets a little busy in the visualizer of all ROIs when multiple ROIs are selected. 

Alternatively, is there a way to have y-axes displayed for the  individual ROIs within the visualizer for all assigned ROIs?

I have tried to use publish subject after the "Photometry Writer" node in order to extract the values for individual ROIs from that, but the output of that in CsvWriter, seems to only consist of some metadata (Attached file: OutputPublishSubjectandCsvWriter), which is different from the CSV file output from the Photometry Writer node (Attached file: OutputPhotometryWriter).

I hope you can help me solve this. 

Thank you in advance for your help.

Best regards
Søren
 

[Gonçalo Lopes]

Hi Søren,

You can use the GroupRegions node to organize the traces into logical groups, down to even single traces if necessary:

GroupRegions · neurophotometrics/neurophotometrics Wiki · GitHub

Another option is to extract the Activity property (right-click on PhotometryData > Output > Activity) and pull individual traces using the Index operator:

You can select individual traces in this way for inspection by changing the value of the index (be careful to not select values outside the range of available ROIs).

Hope this helps.

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[Søren HJ]

Thank you very much Gonçalo.

This was exactly what I needed!

Best
Søren