Open Microscopy Environment

I'm looking for a suitable place to insert information about the histogram transform (boundaries) used to transform the captured 16-bit image to an 8-bit displayed image. I am working with a system for electron microscopy and it is fairly common to have nearly all of your image data in a narrow peak at the lower end of the 16-bit range. To view this on screen, the data is then transformed to 8 bits using an upper and lower bound placed around this peak. These bounds are usually auto-calculated (crop 0.5% of raw histogram on each side or some such) but can be overridden by the user. The bounds for this transformation would be nice to save in the OME file.

So my question - is there a place where such information can be saved in the OME structure, and if not, are there any plans to incorporate it in future versions?

/Uppstrom

Hello Uppstrom,

At present there are no rendering setting stored in the OME file, there are however rendering setting used by the OMERO server.

In the OMERO server each channel has rendering settings. These settings stored on a per-user basis. If you software were to write the data directly to an OMERO server then you could store these values.

In the OME file you can store values in Structured Annotations. This would allow software that knows about your annotations to read the values, and the OMERO server will preserve the annotation. The server would not by default copy your values to the rendering settings, but this step could be achieved post-import using a custom script.

It could be possible in a future OME file schema to move the values from the annotation into the core model.

If you want either of these approaches outlines in full let me know.

Andrew

The structured annotation alternative seems pretty straightforward, will try it,
thank you!

/Uppstrom