re position ROIs at certain stacks
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re position ROIs at certain stacks
 
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Re: re position ROIs at certain stacks
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Re: re position ROIs at certain stacks
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Re: re position ROIs at certain stacks
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I had thought about this in the past while doing FRAP experiments and after the start of this macro by Jan Brocher have used his code as basis for a macro that when you move the ROI it automatically updates the ROI for all following images in the stack and moves automatically to the next image in the stack.
You can change the sensitivity of the repositioning of the ROI by changing the wait(350) at line 61 of the code. Not extensively tested but seems to work. Best wishes Kees Dr Ir K.R. Straatman Senior Experimental Officer Centre for Core Biotechnology Services University of Leicester http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif (notice new website!) -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jan Brocher - BioVoxxel Sent: 04 February 2014 10:10 To: [hidden email] Subject: Re: re position ROIs at certain stacks Hi Pablo, hi Jacob potentially you can check the following macro. It might do, what you need. I simply put it together quickly, so if there is a problem contact me again. What you have to do: 1.) draw the ROI you want to put into the image 2.) choose the color of the ROI using the color picker tool 3.) run the macro I attached here 4.) go through your slices and if you need to manually move a selection do the following 5.) keep [Alt] pressed and click inside your ROI (thus you reactivate it 6.) move it or change its appearance 7.) click somewhere outside the ROI to add it back to the overlay layer 8.) press Ok in the small dialog box --> This will add all the ROIs to teh ROI-Manager and using this one you can select >More >Multi Measure with the choice to measure all slices active and you will get the analyses of all the ROIs in all slices in teh results table. Macro code: /**Macro written by Jan Brocher/BioVoxxel * NO WARRENTY of functionality and no liability for any damages. */ getDimensions(width, height, channels, slices, frames); Dialog.create("ROI setup"); Dialog.addChoice("label:", newArray( "frames", "slices", "channels"), "frames"); Dialog.show(); dimension = Dialog.getChoice(); color = toHex(getValue("rgb.foreground")); run("Overlay Options...", "stroke="+color+" width=0 fill=none set"); setBatchMode(true); if(dimension=="frames") { if(frames<2) { exit("no multiple frames available"); } else { toLabel = frames; } } else if(dimension=="slices") { if(slices<2) { exit("no multiple slices available"); } else { toLabel = slices; } } else if(dimension=="channels") { if(channels<2) { exit("no multiple channels available"); } else { toLabel = channels; } } roiManager("reset"); for(i=1; i<=toLabel; i++) { if(dimension=="frames") { Stack.setFrame(i); } else if(dimension=="slices") { Stack.setSlice(i); } else if(dimension=="channels") { Stack.setChannel(i); } run("Add Selection..."); } //reset Stack position if(dimension=="frames") { Stack.setFrame(1); } else if(dimension=="slices") { Stack.setSlice(1); } else if(dimension=="channels") { Stack.setChannel(1); } setBatchMode(true); //enable manual adjustments to the individual ROIs waitForUser("adjust overlays and press Ok"); run("To ROI Manager"); exit(); //end of macro--------------------------------------------- -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Move_ROI3.txt (3K)
Re: re position ROIs at certain stacks
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Re: re position ROIs at certain stacks
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Re: re position ROIs at certain stacks
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In reply to this post by gankaku
Hi Jan,
OK, took a little more time than I had planned but the attached macro allows you to move the ROI and confirm with a left mouse click outside the ROI its position what will update the positions in the ROI manager of this and all following ROIs. As before not extensively tested but it seems to work. Best wishes Kees Dr Ir K.R. Straatman Senior Experimental Officer Centre for Core Biotechnology Services University of Leicester http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif -----Original Message----- From: Jan Brocher - BioVoxxel [mailto:[hidden email]] Sent: 04 February 2014 17:36 To: [hidden email]; Straatman, Kees (Dr.) Subject: Re: re position ROIs at certain stacks Hi Kees, Nice improvement! one more suggestion to that (since I don't find the time to do it at the moment in the code): Using your macro and changing the ROI position directly moves on to the next slide even without "confirming" the acceptance of the repositioning by adding the overly back due to clciking outside it. This might lead to problems when you would need to reposition the same ROI with several trials. Thus, I would suggest to run the update on the ROIs after the acceptance of the changes by a fina click outside the ROI and then move to the next slice. cheers, Jan -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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