PAR selection

[bvivier]

Is it possible to have more informations about how you select your PAR value? I work with an Imaging PAM with different actinic intensities, what does your PAR = 134 correspond to here?

Thanks!

[PageG]

Hello,

PAR can be specified when processing images using the following core functions. These are the functions you use to calculate the fluorescence parameters from raw images. PAR can be a single value, or a vector (for a rapid light-response curve).

• 'im_pam_tiff': https://github.com/PageG/IM-PAM/blob/master/Functions/im_pam_tiff.m
• 'im_pam_tiff_fvfm': https://github.com/PageG/IM-PAM/blob/master/Functions/im_pam_tiff_fvfm.m

The function 'PROC_single_pam', where PAR is fixed at 134 umol m-2 s-1, is a higher-level function that applies the 'im_pam_tiff_fvfm' and 'seg_leaf' functions to ingest an unprocessed TIFF, calculate the fluorescence parameters and then summarise them for each leaf in the image. If you look at the code for 'PROC_single_pam', you'll see that I mention that you can modify the PAR value as appropriate.

In my case, PAR = 134 was the intensity of the saturating pulse when making a single measurement, so I hard-coded it into the batch-processing function, but it can be easily changed to suit your own purposes.

Have a look at example 3 here, where I used 'im_pam_tiff_fvfm' and specified the PAR as 134: https://pageg.github.io/batch_process_fvfm_example.html

Gerald

[bvivier]

Hello Gerald,

Thank you for your details, in my situation the PAR is a vector (rapid light-response curve), by specifying it in this form, are your functions still usable as is?

Baptiste

[PageG]

Hi Baptiste,

Yes, the 'im_pam_tiff' function accepts a vector of PAR values, along with the TIFF stack. A caveat is that the function was written to read a 640x480 pixel TIFF stack exported from Walz ImagingWin software. If you're using different hardware & software, you may need to modify the code to correctly read the images. You'll also need to make sure the order of the images within the stack is the same as specified within the function (e.g. which layer is Fo, Fm, etc). You'll see those details specified in lines 29 - 42.

Gerald.