Ability to save simcheck results to file for automated processing.

[iandobbie]

We are hoping to automate more checks. Having simcheck automatically save the data in a machine parseable form would be very useful.

[juliomateoslangerak]

I’ve been working on a python (jython) script to run simcheck on a full OMERO dataset.

As for now
-it gets the images from OMERO and pairs them (only tested on dv files)
-runs a choice of simcheck routines
-uploads the results back to the same dataset: resulting images and resulting metrics as key-value pairs.

It runs ok but needs:

• code cleaning
• testing on other file formats
• saving pass/not pass results as keywords
• option to choose a local directory to analyze and import after. That saves time as images are not downloaded.

I don’t know if this is the last version:

https://github.com/juliomateoslangerak/Omero-Imagej-Scripts.git

[juliomateoslangerak]

This is how it looks after. Of course all the numbers are accessible through OMERO's API

[DeboraOlivier]

Hiya, having used the version from Ian https://github.com/iandobbie/Omero-Imagej-Scripts that works really well.
However, is it possible to save the log file somewhere on OMERO as an attachement to the image at all?

[juliomateoslangerak]

Hi,
happy you like it.
As it is now, all the measurements are saved as key-value pairs in OMERO on either the raw or the reconstructed images. That allows automated access through OMERO's API. That is in my eyes more convenient than a text file.
From OMERO version 5.5 you have advanced search features and you may request, for example, all the images that have more than 30% bleaching in channel 1:
C1 total intensity variation (%):[30 TO 100]
or a modulation contrast bellow 10 on any channel:
C? average feature MCNR:[0 TO 10]

Does this feel convenient to you?

What would be the use case where you want a text file attached to the images or dataset?