Hai Everyone,
I am now studying PhD in the final year and one of my research project is about syntheis of zeolites and nanoparticle zeolites. I have a lot of their images from SEM (micrometre) and TEM (nanometre). I want to analyse their particle size. My zeolites are in aggrerates or in clusters form. Honestly, It is making me grazy. I can not measure their particle size and also their particle size distribution. I realy need your help. Because I am a beginner, please tel me the prosedur how to analyse them step by step. Any help is hugely appreciated. Cheers, NZN |
Hi, I am looking for a simple way to quantify single channel fluoresence image on ImageJ. I looked up some previous posts but I would really like a step-by-step approach or a plug-in. Currently, after I convert to a single channel image to binary, ImageJ appears to correctly pick up my fluorescent spots after I threshold as black spots. However, how do I get it to count the number of punctate fluorescent spots on the periphery of the cell and the central cluster of spots as individual particles? ImageJ wants to count the central cluster as "one particle" regardless of the pixel size I set. I am ok with either 'total area of black spots combined' or 'particle number' as a rough indicator of fluorescence. Or if someone knows another free program that can do this better - I would be interested in that as well. Thanks. -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Naz U Din Sent: Wednesday, April 25, 2012 5:12 AM To: [hidden email] Subject: How to measure a particle size of zeolite (micrometre and nanometre) Hai Everyone, I am now studying PhD in the final year and one of my research project is about syntheis of zeolites and nanoparticle zeolites. I have a lot of their images from SEM (micrometre) and TEM (nanometre). I want to analyse their particle size. My zeolites are in aggrerates or in clusters form. Honestly, It is making me grazy. I can not measure their particle size and also their particle size distribution. I realy need your help. Because I am a beginner, please tel me the prosedur how to analyse them step by step. Any help is hugely appreciated. Cheers, NZN The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. |
Hello,
I would refer you to this previous posting first: http://imagej.1557.n6.nabble.com/Quantifying-fluorescence-in-zebrafish-td3683428.html Specifically, it sounds like you have a desire to threshold and segment different parts of your images and then count certain objects. There a many plugins on the ImageJ website that can do this. If you provide more details about what you're trying to quantify and what questions you seek to answer with this data, someone may be able to point you to the right plugin/macro. Alternatively, you could build your own set of automatic processing steps using the macro recorder. John Oreopoulos On 2012-04-25, at 9:33 AM, Ghosh, Papia wrote: > > Hi, > > I am looking for a simple way to quantify single channel fluoresence image on ImageJ. I looked up some previous posts but I would really like a step-by-step approach or a plug-in. > > Currently, after I convert to a single channel image to binary, ImageJ appears to correctly pick up my fluorescent spots after I threshold as black spots. However, how do I get it to count the number of punctate fluorescent spots on the periphery of the cell and the central cluster of spots as individual particles? ImageJ wants to count the central cluster as "one particle" regardless of the pixel size I set. I am ok with either 'total area of black spots combined' or 'particle number' as a rough indicator of fluorescence. > > Or if someone knows another free program that can do this better - I would be interested in that as well. > > Thanks. > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Naz U Din > Sent: Wednesday, April 25, 2012 5:12 AM > To: [hidden email] > Subject: How to measure a particle size of zeolite (micrometre and nanometre) > > Hai Everyone, > > I am now studying PhD in the final year and one of my research project is > about syntheis of zeolites and nanoparticle zeolites. I have a lot of their > images from SEM (micrometre) and TEM (nanometre). I want to analyse their > particle size. > > My zeolites are in aggrerates or in clusters form. Honestly, It is making > me grazy. I can not measure their particle size and also their particle > size distribution. > > I realy need your help. Because I am a beginner, please tel me the > prosedur how to analyse them step by step. > > Any help is hugely appreciated. > > Cheers, > NZN > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. |
There is already a macro written by Pawel Znojek entitled PZFociEz which
does exactly what you want. It can be obtained from his web-site; ImageJ macro for gamma H2AX foci analysis <http://www.pzfociez.com/> at; http://www.pzfociez.com/ However, I have a question in this thread. The macro referred to above identifies fluorescent foci in cell nuclei well, as points marked on the image. However, I would like advice on two problems. How should I count the number of "peaks" or points in each nucleus [an roi in the manager] and how do I exclude occasional peaks outside the roi's. Then how do I write the result to a text file linking the number of peaks counted in each roi to the identity of that roi? With many thanks, Sydney On 25/04/2012 16:14, John Oreopoulos wrote: > Hello, > > I would refer you to this previous posting first: > > http://imagej.1557.n6.nabble.com/Quantifying-fluorescence-in-zebrafish-td3683428.html > > Specifically, it sounds like you have a desire to threshold and segment different parts of your images and then count certain objects. There a many plugins on the ImageJ website that can do this. If you provide more details about what you're trying to quantify and what questions you seek to answer with this data, someone may be able to point you to the right plugin/macro. Alternatively, you could build your own set of automatic processing steps using the macro recorder. > > John Oreopoulos > > > On 2012-04-25, at 9:33 AM, Ghosh, Papia wrote: > >> Hi, >> >> I am looking for a simple way to quantify single channel fluoresence image on ImageJ. I looked up some previous posts but I would really like a step-by-step approach or a plug-in. >> >> Currently, after I convert to a single channel image to binary, ImageJ appears to correctly pick up my fluorescent spots after I threshold as black spots. However, how do I get it to count the number of punctate fluorescent spots on the periphery of the cell and the central cluster of spots as individual particles? ImageJ wants to count the central cluster as "one particle" regardless of the pixel size I set. I am ok with either 'total area of black spots combined' or 'particle number' as a rough indicator of fluorescence. >> >> Or if someone knows another free program that can do this better - I would be interested in that as well. >> >> Thanks. >> -----Original Message----- >> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Naz U Din >> Sent: Wednesday, April 25, 2012 5:12 AM >> To: [hidden email] >> Subject: How to measure a particle size of zeolite (micrometre and nanometre) >> >> Hai Everyone, >> >> I am now studying PhD in the final year and one of my research project is >> about syntheis of zeolites and nanoparticle zeolites. I have a lot of their >> images from SEM (micrometre) and TEM (nanometre). I want to analyse their >> particle size. >> >> My zeolites are in aggrerates or in clusters form. Honestly, It is making >> me grazy. I can not measure their particle size and also their particle >> size distribution. >> >> I realy need your help. Because I am a beginner, please tel me the >> prosedur how to analyse them step by step. >> >> Any help is hugely appreciated. >> >> Cheers, >> NZN >> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and properly >> dispose of the e-mail. -- Professor Sydney Shall, Department of Haematological Medicine, King's College London, Medical School, 123 Coldharbour Lane, LONDON SE5 9NU, Tel& Fax: +44 (0)207 848 5902, E-Mail: sydney.shall, [correspondents outside the College should add; @kcl.ac.uk] www.kcl.ac.uk |
There is a macro for ImageJ written by Pawel Znojek entitled PZFociEz,
which I am using to quantify fluorescent spots in human cell nuclei. The procedure identifies each nucleus with its DAPI stain and circles it as an ROI. Then in a second stage the maxima of fluorescent intensity in each nucleus is identified. This works fine, but I need help on the next step. How should I count the number of "peaks" or maxima, points in each nucleus [an roi in the manager] and how do I exclude occasional peaks outside the roi's. Then how do I write the result to a text file linking the number of peaks counted in each roi to the identity of that roi? The macro is provided at; ImageJ macro for gamma H2AX foci analysis <http://www.pzfociez.com/> or at; http://www.pzfociez.com/ I would greatly appreciate any help. Sydney -- Professor Sydney Shall, Department of Haematological Medicine, King's College London, Medical School, 123 Coldharbour Lane, LONDON SE5 9NU, Tel& Fax: +44 (0)207 848 5902, E-Mail: sydney.shall, [correspondents outside the College should add; @kcl.ac.uk] www.kcl.ac.uk |
On Friday 27 Apr 2012 10:03:24 Shall, Sydney wrote:
> How should I count the number of "peaks" or maxima, points in each > nucleus [an roi in the manager] and how do I exclude occasional peaks > outside the roi's. Then how do I write the result to a text file linking > the number of peaks counted in each roi to the identity of that roi? It is tricky to count objects within objects by default because IJ's model follows that the ROI *is* what you measure and there is no "menu way" to link some ROIs to other ROIS. However, it can be done. One way to do this is using the XStart, YStart points of the objects and use grey integral density to count (by redirection) how many of those are in each particle. To do this process your image to 8bit binary, so the nuclei are all white and the "objects" inside nuclei AND the background are black (so the objects to be counted look like holes in the nuclei). Then look for a macro in the morphology.zip in my page http://www.dentistry.bham.ac.uk/landinig/software/software.html called ParticleHoleNumber.txt That should do it. From that page: ParticleHoleNumber.txt The number of holes per particle is obtained by redirection of the original image with all its holes filled, to a copy of the original image where the holes' starting pixels are set to 1. These pixels (one per hole) are accumulated in the Greyscale Integrated Density column (GrIntDen). You need to have the morphology plugins installed, because the macro uses some of those. Hope it helps. Gabriel |
Thanks Gabriel,
I will try your plugin and let you know how I get on. With many thanks, Sydney On 27/04/2012 11:38, Gabriel Landini wrote: > On Friday 27 Apr 2012 10:03:24 Shall, Sydney wrote: >> How should I count the number of "peaks" or maxima, points in each >> nucleus [an roi in the manager] and how do I exclude occasional peaks >> outside the roi's. Then how do I write the result to a text file linking >> the number of peaks counted in each roi to the identity of that roi? > It is tricky to count objects within objects by default because IJ's model > follows that the ROI *is* what you measure and there is no "menu way" to link > some ROIs to other ROIS. However, it can be done. > > One way to do this is using the XStart, YStart points of the objects and use > grey integral density to count (by redirection) how many of those are in each > particle. > > To do this process your image to 8bit binary, so the nuclei are all white and > the "objects" inside nuclei AND the background are black (so the objects to be > counted look like holes in the nuclei). > Then look for a macro in the morphology.zip in my page > http://www.dentistry.bham.ac.uk/landinig/software/software.html called > ParticleHoleNumber.txt > That should do it. > > From that page: > ParticleHoleNumber.txt The number of holes per particle is obtained by > redirection of the original image with all its holes filled, to a copy of the > original image where the holes' starting pixels are set to 1. These pixels > (one per hole) are accumulated in the Greyscale Integrated Density column > (GrIntDen). > > You need to have the morphology plugins installed, because the macro uses some > of those. Hope it helps. > > Gabriel > -- Professor Sydney Shall, Department of Haematological Medicine, King's College London, Medical School, 123 Coldharbour Lane, LONDON SE5 9NU, Tel& Fax: +44 (0)207 848 5902, E-Mail: sydney.shall, [correspondents outside the College should add; @kcl.ac.uk] www.kcl.ac.uk |
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