Open iandobbie opened 5 years ago
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:
I don’t know if this is the last version:
https://github.com/juliomateoslangerak/Omero-Imagej-Scripts.git
This is how it looks after. Of course all the numbers are accessible through OMERO's API
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?
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?
We are hoping to automate more checks. Having simcheck automatically save the data in a machine parseable form would be very useful.