Feature request OMERO viewer : basic thresholding


In order to develop our software for automation (TAPAS) using OMERO, sometimes we need to input a manual threshold. Here a typical example :

  1. Process data, filters, …
  2. Find manual threshold
  3. Threshold (using previous value) and label
  4. Analysis

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.



Hi Thomas,

Thanks for your feedback. I created an issue at https://github.com/ome/omero-iviewer/issues/288

However, I find that a regular channel colour does a pretty good job as a binary LUT, and you just have to move 2 handles of the slider together instead of a single thresholding handle. If you want to move the slider handles very close together, you can set the cut-off values manually or use the up/down arrows:

I’m not familiar with the thresholding workflow in ImageJ but hopefully this isn’t too much worse?

NB: If you save the rendering settings, you could get those values back via the OMERO API as an alternative to using key-value pairs, although using key-values might have some advantages too.



Hi Will,

Thanks for your feedback, I think I like the idea of having the range of the LUT at one value, I did not think of that.

If you could (and maybe it is not that simple) make that the two sliders move together when a checkbox thresholding is selected in advanced, it would be just perfect !



That sounds like a good solution.