Information relevant to JAVA_HOME related problems: The up-to-date check says: You wanted never to be reminded. Java.vm.name => Java HotSpot(TM) 64-Bit Server VM Information about your version of Java - this information is useful for the Fiji developers: Currently I am running the latest version which does have the changed option. I am quite sure that the change came with the new update of Fiji, I apologise for not being able to give the specific detail. I hope the old option can be restored or at least an alternative option to have the same viewing as in the old editions. The change has so far caused quite some trouble to me, first wasting working time not realizing that the stacks were not registered anymore and second I could not find an option that would allow to overlay of all the point marks regardless of the stack slice property. Now it was changed to: Associate ROIs with Stack positions While in previous versions it stated as option:Īssociate "Show All" ROIs with the stack slices (as also discribed by the help section ( ) By investigating the cause I discovered that the ROI Manager>Option panel was changed significantly. I recently discovered a change in the behaviour of the ROI manager of Fiji, namely that ROI events are by default not any more registered with the slice information. The ROI Manager is basically an overlay with a GUI.I am not sure whether this classifies as bug but in my view it does create un unwanted behaviour by FIJI. Use the Image>Overlay>To ROI Manager command to move the selections in a overlay to the ROI Manager. Use the Image>Overlay>List Elements command to list the selections in an overlay. Activate a selection in an overlay by long pressing on it. You will want to upgrade to the latest daily build (1.49a5), which fixes several bugs related to the Overlay Brush Tool and overlays.Īn overlay in ImageJ is a list of selections that are displayed on the image. Instead, use the Selection Brush Tool, available by right clicking on the Oval Tool icon, and add each selection to the overlay by pressing "b" (Image>Overlay>Add Selection). The Overlay Brush Tool, available via the toolbar's ">" menu, is a drawing tool not suited for creating selections. I'd like to threshold based on the intensity under each overlay therefore it must become an ROI first, the overlay is purely to select parts of the image for further analysis. I tried Image>Overlay>To ROI Manager but this doesn't seem to treat each overlay the same as it would a regular selection. As ImageJ only supports one selection/ROI at a time could i use the overlay brush tool to paint over various points (if i use a large ish brush diameter) then convert these to ROI's or at least use the ROI manager to select each overlay in turn then make it an ROI-analyse it then move on to the next. I'd like to be able to isolate areas of a fluorescence image to work on and there a few points of interest.
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