In order to develop our software for automation (TAPAS) using OMERO, sometimes we need to input a manual threshold. Here a typical example :
- Process data, filters, …
- Find manual threshold
- Threshold (using previous value) and label
Steps 1, 3 and 4 are fully automated and in order to automate step 3 we enter a manual threshold in key-value pair and use this information to do the thresholding.
For step 2 we usually download the data, find threshold in ImageJ, but if the data is big it is not optimal.
I found an alternative in OMERO viewer using the red-green LUT and adjust the sliders in order to get kinda threshold. I would prefer to have a proper binary LUT or better a proper thresholding tool in OMERO.