Software to find the area of a shape in an image
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Daniel Brewer ★ 1.9k
@daniel-brewer-1791
Last seen 7.7 years ago
Hi, We have a series of tissue slices that have tumour within them and we would like to quantify the area within each slice that is occupied by tumour. Is there a cheap or free program that will assist in this? either by automatically looking for colours or for a user to manual draw round a shape and it give you the area? Not exactly bioconductor related but the idea is to quantify this and then do various bioinformatics on it. Hope you forgive me. Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}
Cancer Cancer • 961 views
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Susan Holmes ▴ 120
@susan-holmes-158
Last seen 7.7 years ago
Daniel, Gemident is available for this type of task, see http://www.jstatsoft.org/v30/i10 for article and www.gemident.com for the software and demos, it should automatically segment your picture. Best Susan Holmes Statistics Stanford On Wed, 22 Jul 2009, Daniel Brewer wrote: > Hi, > > We have a series of tissue slices that have tumour within them and we > would like to quantify the area within each slice that is occupied by > tumour. Is there a cheap or free program that will assist in this? > either by automatically looking for colours or for a user to manual draw > round a shape and it give you the area? > > Not exactly bioconductor related but the idea is to quantify this and > then do various bioinformatics on it. Hope you forgive me. > > Thanks > > > Dan > > -- > ************************************************************** > Daniel Brewer, Ph.D. > > Institute of Cancer Research > Molecular Carcinogenesis > Email: daniel.brewer at icr.ac.uk > ************************************************************** > > The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. > > This e-mail message is confidential and for use by the a...{{dropped:2}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Ludo Muller ▴ 50
@ludo-muller-2991
Last seen 7.7 years ago
Hi Dan, You can try CellProfiler www.cellprofiler.org), open source software that allows analysis of cell/tissue images. One of their examples is actually a pipeline for the detection of tumors in mouse lungs. Cheers, Ludo. --- Ludo A.H. Muller, Ph.D. University of Coimbra Centre for Functional Ecology Cal?ada Martim de Freitas 3001-455 Coimbra Portugal Telephone: +351 239 85 52 49 Fax: +351 239 85 52 11 E-mail: ludo.muller at duke.edu Hi, We have a series of tissue slices that have tumour within them and we would like to quantify the area within each slice that is occupied by tumour. Is there a cheap or free program that will assist in this? either by automatically looking for colours or for a user to manual draw round a shape and it give you the area? Not exactly bioconductor related but the idea is to quantify this and then do various bioinformatics on it. Hope you forgive me. Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:15}}
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Laurent Gautier ★ 2.3k
@laurent-gautier-29
Last seen 7.7 years ago
Did you already check the bioconductor package EBImage ? HTH, L. Daniel Brewer wrote: > Hi, > > We have a series of tissue slices that have tumour within them and we > would like to quantify the area within each slice that is occupied by > tumour. Is there a cheap or free program that will assist in this? > either by automatically looking for colours or for a user to manual draw > round a shape and it give you the area? > > Not exactly bioconductor related but the idea is to quantify this and > then do various bioinformatics on it. Hope you forgive me. > > Thanks > > > Dan >
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@jordi-altirriba-gutierrez-682
Last seen 3.2 years ago
Hi Daniel, I don't really think that it is a BioC related question, nevertheless here are my comments. Have you tried ImageJ? There is a version with many plugins in MacBiophotonics. Just for free: http://www.macbiophotonics.ca/downloads.htm If you are using an automatic slide in your microscope, in my case a Leica microscope, you can take many photos of all an area, an the Leica program puts one next to the other automatically. If you want take a photo of all the slide (23x76mm), you should take photos at 10x. If you are taking photos from a core (2mm diameter) you can take them at 40x. If you have big images [100-300 Mb] (as the one obtained after taking 56 photos at 40x from a core of 2mm diameter and joined together to form a unique image), I would recommend to work under a 64bits platform and get a minimun of 4Gb of RAM. If it is not the case, you can work under a 32bits system, with quite less RAM. Good luck! Jordi Altirriba Hospital Clinic Barcelona Spain Message: 4 Date: Wed, 22 Jul 2009 14:48:10 +0100 From: Daniel Brewer <daniel.brewer@icr.ac.uk> Subject: [BioC] Software to find the area of a shape in an image To: Bioconductor mailing list <bioconductor@stat.math.ethz.ch> Message-ID: <4A67189A.2050304@icr.ac.uk> Content-Type: text/plain; charset=ISO-8859-1 Hi, We have a series of tissue slices that have tumour within them and we would like to quantify the area within each slice that is occupied by tumour. Is there a cheap or free program that will assist in this? either by automatically looking for colours or for a user to manual draw round a shape and it give you the area? Not exactly bioconductor related but the idea is to quantify this and then do various bioinformatics on it. Hope you forgive me. Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer@icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:9}}
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Well, it is not a bioconductor question, but depending on data analyzed it can be a very relevant question. If you work in R and want to integrate image analysis and object detection into your R-script workflow, then the above mentioned EBImage is something you should try. It contains numerous examples, on object detection and feature extraction as well. It incorporates pretty much everything of CellProfiler and many functions found in ImageJ adding a bunch of its own. The best side of it is that you can actually script any of the analysis and image processing so that you can apply it to thousands of images objectively. Well, this can also be seen as its worst part -- apart from image display and browser there is no GUI, it is all scripting ;) Runs on any platform tested so far, MS Windows, Linux 32/64bit, MacOS both from source and as binary. We developed it to analyze full genome microscopy assays with more than 500K images. The memory point is valid: you will probably need a 64bit Linux system to run any large-scale image analysis due to memory requirements, but this is up to you, this is not a problem of any particular software. Best of luck, Oleg Jordi Altirriba Guti?rrez wrote: > Hi Daniel, > > > > I don't really think that it is a BioC related question, nevertheless here are my comments. > > > > Have you tried ImageJ? > > There is a version with many plugins in MacBiophotonics. Just for free: > > > > http://www.macbiophotonics.ca/downloads.htm > > > > If you are using an automatic slide in your microscope, in my case a Leica microscope, you can take many photos of all an area, an the Leica program puts one next to the other automatically. If you want take a photo of all the slide (23x76mm), you should take photos at 10x. If you are taking photos from a core (2mm diameter) you can take them at 40x. > > > > If you have big images [100-300 Mb] (as the one obtained after taking 56 photos at 40x from a core of 2mm diameter and joined together to form a unique image), I would recommend to work under a 64bits platform and get a minimun of 4Gb of RAM. If it is not the case, you can work under a 32bits system, with quite less RAM. > > > > Good luck! > > > > Jordi Altirriba > > Hospital Clinic > > Barcelona > > Spain > > > > Message: 4 > Date: Wed, 22 Jul 2009 14:48:10 +0100 > From: Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> > Subject: [BioC] Software to find the area of a shape in an image > To: Bioconductor mailing list <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <4A67189A.2050304 at icr.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > We have a series of tissue slices that have tumour within them and we > would like to quantify the area within each slice that is occupied by > tumour. Is there a cheap or free program that will assist in this? > either by automatically looking for colours or for a user to manual draw > round a shape and it give you the area? > > Not exactly bioconductor related but the idea is to quantify this and > then do various bioinformatics on it. Hope you forgive me. > > Thanks > > > Dan > >
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