Spatial and area data in ImageJ
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Spatial and area data in ImageJ
 
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G'day All from sunny Tasmania,
I have been using ImageJ for years (and NIH Image before that...) to do simple tasks like measure areas, perimeters of leaves etc. But now I want to do something a little more complex and I'm afraid I am stuck and would appreciate some assistance. I want ImageJ to find particles (easy), measure their area (again easy) and then spit out a list of the x,y coordinates for each particle (centroid I guess) with its area (this is what I can't do). Any help on this would be great. Thanks and all the best Mark A/Prof. Mark Hovenden Locked Bag 55 School of Plant Science Hobart Tas. 7001 University of Tasmania Australia phone: +61 3 6226 7874 fax: +61 3 6226 2698 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear Mark
When you find the particles add them to the ROI manager, don't need to display anything. In Analyze > Set Measurements select Area and centroid. In the ROI manager menu click on More>> and select Multi Measure. Deselect "One Row Per Slice" and click OK. This should give you a list of Area and X and Y coordinates. Hope this is what you had in mind. Kees Dr Ir K.R. Straatman Senior Experimental Officer Centre for Core Biotechnology Services University of Leicester http://www.le.ac.uk/biochem/microscopy/home.html -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Mark Hovenden Sent: 08 October 2012 04:13 To: [hidden email] Subject: Spatial and area data in ImageJ G'day All from sunny Tasmania, I have been using ImageJ for years (and NIH Image before that...) to do simple tasks like measure areas, perimeters of leaves etc. But now I want to do something a little more complex and I'm afraid I am stuck and would appreciate some assistance. I want ImageJ to find particles (easy), measure their area (again easy) and then spit out a list of the x,y coordinates for each particle (centroid I guess) with its area (this is what I can't do). Any help on this would be great. Thanks and all the best Mark A/Prof. Mark Hovenden Locked Bag 55 School of Plant Science Hobart Tas. 7001 University of Tasmania Australia phone: +61 3 6226 7874 fax: +61 3 6226 2698 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Spatial and area data in ImageJ
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Hello,
This is a very useful feature, and I was wondering whether it is possible to include this in a macro? When performing this operation while recording a macro, it is only included in the Recorder when the box at 'one row per slice' is checked. However, I need to get a list in which every ROI has its own row. By the way, I've been doing this using the following code until now: ROIcount = roiManager("count"); for (i=0; i<ROIcount; i++) { roiManager("select", i); roiManager("Measure"); } Would it actually make a difference with the Multi Measure option? Thanks, Rachel -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Straatman, Kees R. (Dr.) Sent: Monday, October 08, 2012 9:44 AM To: [hidden email] Subject: Re: Spatial and area data in ImageJ Dear Mark When you find the particles add them to the ROI manager, don't need to display anything. In Analyze > Set Measurements select Area and centroid. In the ROI manager menu click on More>> and select Multi Measure. Deselect "One Row Per Slice" and click OK. This should give you a list of Area and X and Y coordinates. Hope this is what you had in mind. Kees Dr Ir K.R. Straatman Senior Experimental Officer Centre for Core Biotechnology Services University of Leicester http://www.le.ac.uk/biochem/microscopy/home.html -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Mark Hovenden Sent: 08 October 2012 04:13 To: [hidden email] Subject: Spatial and area data in ImageJ G'day All from sunny Tasmania, I have been using ImageJ for years (and NIH Image before that...) to do simple tasks like measure areas, perimeters of leaves etc. But now I want to do something a little more complex and I'm afraid I am stuck and would appreciate some assistance. I want ImageJ to find particles (easy), measure their area (again easy) and then spit out a list of the x,y coordinates for each particle (centroid I guess) with its area (this is what I can't do). Any help on this would be great. Thanks and all the best Mark A/Prof. Mark Hovenden Locked Bag 55 School of Plant Science Hobart Tas. 7001 University of Tasmania Australia phone: +61 3 6226 7874 fax: +61 3 6226 2698 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi,
Multi Measure is much faster than your code, but indeed, it does not work in a macro. Results are for both the same. Wayne, is this something that can be implemented? Best wishes Kees -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Nilwik Rachel (BW) Sent: 08 October 2012 09:30 To: [hidden email] Subject: Re: Spatial and area data in ImageJ Hello, This is a very useful feature, and I was wondering whether it is possible to include this in a macro? When performing this operation while recording a macro, it is only included in the Recorder when the box at 'one row per slice' is checked. However, I need to get a list in which every ROI has its own row. By the way, I've been doing this using the following code until now: ROIcount = roiManager("count"); for (i=0; i<ROIcount; i++) { roiManager("select", i); roiManager("Measure"); } Would it actually make a difference with the Multi Measure option? Thanks, Rachel -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Straatman, Kees R. (Dr.) Sent: Monday, October 08, 2012 9:44 AM To: [hidden email] Subject: Re: Spatial and area data in ImageJ Dear Mark When you find the particles add them to the ROI manager, don't need to display anything. In Analyze > Set Measurements select Area and centroid. In the ROI manager menu click on More>> and select Multi Measure. Deselect "One Row Per Slice" and click OK. This should give you a list of Area and X and Y coordinates. Hope this is what you had in mind. Kees Dr Ir K.R. Straatman Senior Experimental Officer Centre for Core Biotechnology Services University of Leicester http://www.le.ac.uk/biochem/microscopy/home.html -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Mark Hovenden Sent: 08 October 2012 04:13 To: [hidden email] Subject: Spatial and area data in ImageJ G'day All from sunny Tasmania, I have been using ImageJ for years (and NIH Image before that...) to do simple tasks like measure areas, perimeters of leaves etc. But now I want to do something a little more complex and I'm afraid I am stuck and would appreciate some assistance. I want ImageJ to find particles (easy), measure their area (again easy) and then spit out a list of the x,y coordinates for each particle (centroid I guess) with its area (this is what I can't do). Any help on this would be great. Thanks and all the best Mark A/Prof. Mark Hovenden Locked Bag 55 School of Plant Science Hobart Tas. 7001 University of Tasmania Australia phone: +61 3 6226 7874 fax: +61 3 6226 2698 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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