<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Thomas,<div class=""><br class=""></div><div class=""> I’m afraid the features you’re wanting aren’t implemented currently, although they have been requested before.</div><div class=""><br class=""></div><div class="">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</div><div class="">image available on the client side.</div><div class=""><br class=""></div><div class="">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.</div><div class="">However, we know that this fails with large images, due to memory issues.</div><div class="">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.</div><div class=""><br class=""></div><div class="">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.</div><div class="">This still provides a good impression of the pixel intensity distribution, without loading all the raw data for a plane.</div><div class="">You can see a prototype of this at:</div><div class=""><a href="http://will-moore.github.io/weblabs/canvas_rendering/" class="">http://will-moore.github.io/weblabs/canvas_rendering/</a></div><div class=""><br class=""></div><div class="">However, this still only uses a single plane from the image, ignoring other Z-sections and Time points.</div><div class="">But perhaps this would be enough to provide you with a guide for adjusting rendering settings?</div><div class=""><br class=""></div><div class="">You can copy and paste rendering settings between images in OMERO, and can also apply the same rendering</div><div class="">settings to all images in a dataset or across multiple datasets to compare different experimental conditions. </div><div class="">E.g. right-click on an image > Rendering Settings > Copy</div><div class="">Then select a Dataset (image container) in the Tree, right-click > Rendering Settings > Paste</div><div class=""><br class=""></div><div class=""> Let us know if that workflow helps, and if the prototype above is close to what you’re looking for.</div><div class=""><br class=""></div><div class=""> Cheers,</div><div class=""><br class=""></div><div class=""> Will.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 16 Dec 2015, at 12:44, Thomas Julou <<a href="mailto:thomas.julou@normalesup.org" class="">thomas.julou@normalesup.org</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">Hello,<br class=""><br class="">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?<br class=""><br class="">This is particularly needed to adjust the contrast of a dataset and/or to compare different experimental conditions.<br class="">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).<br class=""><br class="">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,<br class=""><br class="">--<br class="">Thomas Julou | Computational & Systems Biology | Biozentrum – University of Basel | Klingelbergstrasse 50/70 CH-4056 Basel | +41 (0)61 267 16 21<br class=""><br class="">_______________________________________________<br class="">ome-users mailing list<br class=""><a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a><br class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br class=""></div></blockquote></div><br class=""></div></body></html>