Closed pauladkisson closed 4 months ago
Linking the reference_frame
question from #20:
The reference_frame is a description of the "zero-position" for a Spatial Series like the mouse's position or orientation. For example, "top left", "bottom right", etc.
The question then being what our reference frame is for position/orientation columns in the parquet files.
@kaijfox, please see new questions about extra raw data. Thanks!
Hi @pauladkisson, I can attempt to answer these questions in bits and pieces over time.
I'll start with the first section - optoda_raw_data/closed_loop_behavior.parquet
experiment_types
: excitation
is the main closed-loop reinforcement experiment we performed (see fig. 3a-d for setup); excitation_photometry
is the same experimental setup as excitation
but in animals what we also measured dLight in (also related to fig. 3a-d); excitation_pulsed
follows the same experimental protocol as the closed-loop reinforcement experiment, but we performed ~25Hz pulsed stimulation for 3s instead of the default 250ms continuous stimulation (see fig. 3m).feedback_status
refers to stimulation onset. A value of 1 = stimulation, 0 = catch trial (i.e., we detected the target, but didn't stim), -1 = everything elseuuid
associated with them. If after you've verified that there are sessions with the same uuid
but different target_syllable
s, what is likely happening is that the session is on a recording day that occurred between the two stim sessions for that week. We duplicate those sessions in the dataframe to group "session sequences" (where a sequence contains pre-stim, stim, and post-stim sessions for a target syllable) more easily, and the middle session is the only one shared with both stim sessions (i.e., post-stim for 1 sequence, pre-stim for the other).Next, the video files section:
depth.avi
file contains the raw depth video collected during a session. This means the value associated with each pixel corresponds to the distance the camera is from that point in physical space in millimeters. Thus the mouse won't be clearly visible without some pre-processing. The results_00.mp4
files are a visualization of the extraction process, and thus have intentionally isolated the mouse from the rest of the environment. The ir.avi
file is only used for aligning the photometry signal to behavior.Hey @wingillis,
Thank you for the clarifications! For the experiment_type
, is there a difference between excitation_photometry
and reinforcement_photometry
?
Linking the
reference_frame
question from #20:
Circling back around to this. Based on moseq-extract code it seems like the reference is 'top left' of the image, but could use a confirmation.