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codercahol / chlamy-ImPi

An image processing pipeline for time-series of Chlamydomonas reinhardtii fluorescence photos
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Meaning of the timestep dimension in the tif images #3

Closed murraycutforth closed 9 months ago

murraycutforth commented 9 months ago

I'm not sure exactly what this comment below means, I can see that along the time step dimension the frames of the tif image seem to divide into pairs (is this the pre- and post- saturating pulse measurement?). Is it correct to compute thresholds and masks by averaging all the F0 and Fm values together?

    # should be the number of images divided by 2::Int bc we have F0 and Fm
    NUM_TIMESTEPS = tif.shape[0]
codercahol commented 9 months ago

Two images are taken at for each "data sample". The sampling happens at regular intervals (15 min, iirc).

Yes, the images are pre- and post-saturating pulse measurements. See here for more info: https://en.wikipedia.org/wiki/Plant_stress_measurement#Fv/Fm

technically, only the first pair are "F0" and "Fm" all the subsequent tests are F0' ("F nought prime") and Fm', because the cells are no longer dark adapted.

codercahol commented 9 months ago

with regards to averaging over all F0 and Fm for the masks: in my current code, I compute the thresholds for the light and dark separately and apply them over every other image to the F0 and Fm values. This was either buried in one of the other largely identical sample scripts or I forgot to commit it till just now :)

but here is the source: https://github.com/codercahol/chlamy-ImPi/blob/597c8e4dbb93b62c0f8ef06406db4258ce5f92d0/chlamy_impi/controls_2.py#L105-L117

codercahol commented 9 months ago

closing bc I'm assuming the real issue is the confusion with the comment as discussed in issue #4 and the separate averaging over the F0 and Fm images is already implemented