[ome-users] displaying histogram to adjust the intensity

[William Moore]

Hi Thomas,

 I’m afraid the features you’re wanting aren’t implemented currently, although they have been requested before.

The challenge we have for OMERO compared to the other tools you mentioned is that we don’t have all the raw pixel data for the
image available on the client side.

You are correct: when you draw a ROI in Insight, we do load all the pixel data for the ROI to construct a histogram and calculate other parameters.
However, we know that this fails with large images, due to memory issues.
Also, this only gives you a histogram for the image plane that you are currently viewing, not all the pixels in a multi-plane Z-stack or Time lapse image.

One approach we have been looking at is to provide an "8-bit histogram", using the rendered image pixel values instead of the raw data.
This still provides a good impression of the pixel intensity distribution, without loading all the raw data for a plane.
You can see a prototype of this at:
http://will-moore.github.io/weblabs/canvas_rendering/ <http://will-moore.github.io/weblabs/canvas_rendering/>

However, this still only uses a single plane from the image, ignoring other Z-sections and Time points.
But perhaps this would be enough to provide you with a guide for adjusting rendering settings?

You can copy and paste rendering settings between images in OMERO, and can also apply the same rendering
settings to all images in a dataset or across multiple datasets to compare different experimental conditions. 
E.g. right-click on an image > Rendering Settings > Copy
Then select a Dataset (image container) in the Tree, right-click > Rendering Settings > Paste

  Let us know if that workflow helps, and if the prototype above is close to what you’re looking for.

 Cheers,

  Will.



> On 16 Dec 2015, at 12:44, Thomas Julou <thomas.julou at normalesup.org> wrote:
> 
> Hello,
> 
> I finally start using omero more extensively. One thing I really lack compared to other tools (in particular fiji, icy and micromanager) is the possibility to easily view the intensity histogram of an image. As far as I understand it’s possible only in omero.insight and requires to create a roi for the entire image, correct?
> 
> This is particularly needed to adjust the contrast of a dataset and/or to compare different experimental conditions.
> I’d love to see the histogram displayed in the preview pane of omero web (e.g. one coloured line per displayed channel, with a checkbox for log y-axis). Along the same line having a field to set saturation next to the min/max button would be really convenient (similar to the ignore field in micromanager, or to the Auto button in the contrast window of imagej).
> 
> Please let me know if these features are already implemented and I wasn’t able to find them. Otherwise, I’d really like to know whether this is on your roadmap. Best regards,
> 
> --
> Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 267 16 21
> 
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