Omero-Metrics sometimes finds just one bead and then raises and error trying to create the average.

[iandobbie]

We have a dataset that is from a light sheet instrument and it is currently not finding many beads. In these two files it only finds one valid bead and in the web interface raises and error

Opps! something happened
'average_bead'"

And in the omeroweb log file we get nothing of use except that there is only a single valid bead.

``
Image 1002 processed. 0 beads considered valid. 0 beads considered lateral edge. 0 beads considered self proximity. 0 beads considered axial edge. 0 beads considered intensity outlier. 1 beads considered bad fit in z. 0 beads considered bad fit in y. 0 beads considered bad fit in x.
2025-12-16 14:33:58,344 INFO [ microscopemetrics] (proc.63984) analyse_psf_beads():717 Processing image 1004...
2025-12-16 14:34:14,895 INFO [ omero.gateway] (proc.63976) connect():2302 created connection (uuid=1dbc4683-2bdc-484c-8917-3615f5703d15)
2025-12-16 14:34:14,897 INFO [ omero.gateway] (proc.63976) close():2004 closed connection (uuid=None)
2025-12-16 14:34:22,784 INFO [ microscopemetrics] (proc.63984) analyse_psf_beads():737 Image 1004 processed. 1 beads considered valid. 0 beads considered lateral edge. 0 beads considered self proximity. 0 beads considered axial edge. 0 beads considered intensity outlier. 0 beads considered bad fit in z. 0 beads considered bad fit in y. 0 beads considered bad fit in x.

[juliomateoslangerak]

This is intended but maybe not too well thought through. The idea of generating an average bead of a single bead seems odd to me.

[iandobbie]

I agree an average of a single bead is not sensible, however if no valid beads are found the analysis drops out at and earlier point and tell you that no beads were found. If a single valid bead is found then the process producses a "sucess" screen with summary of beads found, how many are rejected for what reason, but then the processing dies and NONE of the output is properly saved, so you don't know why things failed unless you pay a lot of attention when processing.

I suggest that we adjust the microscopemetrics code to produce a valid average even if only one valid bead is found. Maybe we should also produce a warning in these circumstances.

I thunk the edits in microsocpemetrics is very minor, just chnage line 65 of psf_beads.py to

if group.considered_valid.sum() < 1:

rather than < 2.