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sollan / alma

Fully automated (rodent) limb motion analysis toolbox for behavioral analysis with bodypart coordinate data, building upon markerless pose estimation.
GNU General Public License v3.0
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Start Parameter Extraction Errors #43

Open KaryneRabey opened 5 months ago

KaryneRabey commented 5 months ago

We are getting errors when doing kinematic analysis using the spontaneous walking setup.

When we analyze a mouse walking right, we get this error: OCN177_R1_DLC_resnet50_MouseModelFeb3shuffle7_1000000.csv Alma error right

When we analyze a mouse walking left, we get this error: OCN177_L1_DLC_resnet50_MouseModelFeb3shuffle7_1000000.csv Alma error left

What is going wrong here could you please help us, thanks!

sollan commented 5 months ago

Hi,

It looks like there's something wrong with the step cycle detection (only one step cycle in leftwards walk, no step cycle in rightwards walk; whereas in the data I think there should be 4~5 steps). This is most likely a result from your configurations in config.yaml, in particular the "pixels_percm" parameter (i.e., 1 pixel / frame = x_ cm / s). But it might also be caused by setting a different frame rate in config.yaml as the one used for recording.

Have you tried setting no_outlier_filter: True and dragging_filter: False in config.yaml? If there's an issue with the "pixels_per_cm" calculation, these settings should help you debug the issue by disabling the outlier filters (which discard step cycles that are unlikely to happen in reality, such as steps with an extra long stride length.) But eventually, "pixels_per_cm" needs to be correct to obtain meaningful results.

Best, Annette