Plugin error when extracting PSFs too close together

[clairemitchell308]

Hello

I wanted to report some behaviour of your plugin. It's not necessarily an issue but is maybe something to be aware of.

If points are closer together than the PSF box size then the plugin will only measure one of the points. "Extract PSFs" runs with no error, the problem comes when saving, it looks like you have built in some check to compare the number of points against the number of measurements. In the case outlined above there are fewer measurements than there are points so then upon trying to save the error ValueError: Length of values (xx) does not match length of index (yy) appears where xx is less than yy and the save cannot complete.

Obviously most people aren't going to try to fit points so close together but it's not always obvious when selecting points exactly how big the PSF box will be without a scale bar. So maybe a warning box or something should appear to warn users if they try this?

I realised because my automatic bead finding script was excluding points too close together based on euclidean distance, so at points where my beads were diagonally close together they were not being excluded by my script. I have now fixed this and included a buffer where the distance threshold is larger than the PSF box size and now it seems to work okay.

Thanks a lot
Claire

[tibuch]

Hi @clairemitchell308,

Thank you for reporting this. This might be a bug and I will have a look.

Best wishes!