ridge detection
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Dear all while this is probably a more specific question to thorsten
wagner, does anybody now what is the problem when the plugin tells you : " Ah, zwei hauptlinien, das geht nicht ..." Wich basically means that you can not get two principal lines by means of the plugin, while if you ignore this statement by pressing OK the calculation goes on and you get the expected result. I'm using this approach for the analysis of actin stress fibers and it gives good results, but this message is quite a problem particularly if you want to integrate the analysis into a batch process. Thank you for any comment on this, Fabrice. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear Fabrice,
thanks for reporting! Fixed in the latest release. Just update via biomedgroup update site or download it here: https://github.com/thorstenwagner/ij-ridgedetection/releases/tag/v1.1.4 Cheers, Thorsten Am Donnerstag, den 10.12.2015, 11:16 +0100 schrieb Fabrice Senger: > Dear all while this is probably a more specific question to thorsten > wagner, does anybody now what is the problem when the plugin tells > you : > > " Ah, zwei hauptlinien, das geht nicht ..." > > Wich basically means that you can not get two principal lines by > means of > the plugin, while if you ignore this statement by pressing OK the > calculation goes on and you get the expected result. > > I'm using this approach for the analysis of actin stress fibers and > it > gives good results, but this message is quite a problem particularly > if you > want to integrate the analysis into a batch process. > > Thank you for any comment on this, > > Fabrice. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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I have different question about ridge detection plugin.
1) I'd like to know the total length of a ridge, not just of each segments. 2) I'd like to be able to call upon the results data of "Contours" window and save them as a variable in a macro. I can't use getResult function because the table isn't a Results window. Thank you in advance. Sho Fujisawa Molecular Cytology Core Facility Memorial Sloan-Kettering Cancer Center 415 E. 68th St. Z-1840 New York, NY 10065 (646) 888-2186 ________________________________________ From: ImageJ Interest Group [[hidden email]] on behalf of Thorsten Wagner [[hidden email]] Sent: Thursday, December 10, 2015 5:37 AM To: [hidden email] Subject: Re: ridge detection Dear Fabrice, thanks for reporting! Fixed in the latest release. Just update via biomedgroup update site or download it here: https://github.com/thorstenwagner/ij-ridgedetection/releases/tag/v1.1.4 Cheers, Thorsten Am Donnerstag, den 10.12.2015, 11:16 +0100 schrieb Fabrice Senger: > Dear all while this is probably a more specific question to thorsten > wagner, does anybody now what is the problem when the plugin tells > you : > > " Ah, zwei hauptlinien, das geht nicht ..." > > Wich basically means that you can not get two principal lines by > means of > the plugin, while if you ignore this statement by pressing OK the > calculation goes on and you get the expected result. > > I'm using this approach for the analysis of actin stress fibers and > it > gives good results, but this message is quite a problem particularly > if you > want to integrate the analysis into a batch process. > > Thank you for any comment on this, > > Fabrice. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html ===================================================================== Please note that this e-mail and any files transmitted from Memorial Sloan Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi there,
the plugin outputs ROI's, from there you can create a new image with the dimensions of the initial one and draw the ROI's, this gives you allmost the binary segemented image. Maybe you can next use analyse skeleton and extract the parameters you're looking for. All the best, Fabrice. 2015-12-16 19:06 GMT+01:00 Sho Fujisawa <[hidden email]>: > I have different question about ridge detection plugin. > > 1) I'd like to know the total length of a ridge, not just of each segments. > > 2) I'd like to be able to call upon the results data of "Contours" window > and save them as a variable in a macro. I can't use getResult function > because the table isn't a Results window. > > Thank you in advance. > > Sho Fujisawa > Molecular Cytology Core Facility > Memorial Sloan-Kettering Cancer Center > 415 E. 68th St. Z-1840 > New York, NY 10065 > (646) 888-2186 > ________________________________________ > From: ImageJ Interest Group [[hidden email]] on behalf of Thorsten > Wagner [[hidden email]] > Sent: Thursday, December 10, 2015 5:37 AM > To: [hidden email] > Subject: Re: ridge detection > > Dear Fabrice, > > thanks for reporting! Fixed in the latest release. Just update via > biomedgroup update site or download it here: > https://github.com/thorstenwagner/ij-ridgedetection/releases/tag/v1.1.4 > > Cheers, > Thorsten > > Am Donnerstag, den 10.12.2015, 11:16 +0100 schrieb Fabrice Senger: > > Dear all while this is probably a more specific question to thorsten > > wagner, does anybody now what is the problem when the plugin tells > > you : > > > > " Ah, zwei hauptlinien, das geht nicht ..." > > > > Wich basically means that you can not get two principal lines by > > means of > > the plugin, while if you ignore this statement by pressing OK the > > calculation goes on and you get the expected result. > > > > I'm using this approach for the analysis of actin stress fibers and > > it > > gives good results, but this message is quite a problem particularly > > if you > > want to integrate the analysis into a batch process. > > > > Thank you for any comment on this, > > > > Fabrice. > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > ===================================================================== > > Please note that this e-mail and any files transmitted from > Memorial Sloan Kettering Cancer Center may be privileged, > confidential, > and protected from disclosure under applicable law. If the reader of > this message is not the intended recipient, or an employee or agent > responsible for delivering this message to the intended recipient, > you are hereby notified that any reading, dissemination, distribution, > copying, or other use of this communication or any of its attachments > is strictly prohibited. If you have received this communication in > error, please notify the sender immediately by replying to this > message > and deleting this message, any attachments, and all copies and backups > from your computer. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Sho Fujisawa
Dear Sho,
> 1) I'd like to know the total length of a ridge, not just of each > segments. If you have SLOPE overlap resolution activated, it will try to merge the segments to complete ridges. However, at the moment the slope resolution is a little bit buggy: https://github.com/thorstenwagner/ij-ridgedetection/issues > 2) I'd like to be able to call upon the results data of "Contours" > window and save them as a variable in a macro. I can't use getResult > function because the table isn't a Results window. In 1.1.7 it is a Results window: https://github.com/thorstenwagner/ij-ridgedetection/releases/tag/v1.1.7 Please update via biomedgroup update site. Cheers, Thorsten > Thank you in advance. > > Sho Fujisawa > Molecular Cytology Core Facility > Memorial Sloan-Kettering Cancer Center > 415 E. 68th St. Z-1840 > New York, NY 10065 > (646) 888-2186 > ________________________________________ > From: ImageJ Interest Group [[hidden email]] on behalf of > Thorsten Wagner [[hidden email]] > Sent: Thursday, December 10, 2015 5:37 AM > To: [hidden email] > Subject: Re: ridge detection > > Dear Fabrice, > > thanks for reporting! Fixed in the latest release. Just update via > biomedgroup update site or download it here: > https://github.com/thorstenwagner/ij-ridgedetection/releases/tag/v1.1 > .4 > > Cheers, > Thorsten > > Am Donnerstag, den 10.12.2015, 11:16 +0100 schrieb Fabrice Senger: > > Dear all while this is probably a more specific question to > > thorsten > > wagner, does anybody now what is the problem when the plugin tells > > you : > > > > " Ah, zwei hauptlinien, das geht nicht ..." > > > > Wich basically means that you can not get two principal lines by > > means of > > the plugin, while if you ignore this statement by pressing OK the > > calculation goes on and you get the expected result. > > > > I'm using this approach for the analysis of actin stress fibers and > > it > > gives good results, but this message is quite a problem > > particularly > > if you > > want to integrate the analysis into a batch process. > > > > Thank you for any comment on this, > > > > Fabrice. > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > ===================================================================== > > Please note that this e-mail and any files transmitted from > Memorial Sloan Kettering Cancer Center may be privileged, > confidential, > and protected from disclosure under applicable law. If the > reader of > this message is not the intended recipient, or an employee or > agent > responsible for delivering this message to the intended > recipient, > you are hereby notified that any reading, dissemination, > distribution, > copying, or other use of this communication or any of its > attachments > is strictly prohibited. If you have received this communication > in > error, please notify the sender immediately by replying to this > message > and deleting this message, any attachments, and all copies and > backups > from your computer. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by fabrice senger-2
Dear Fabrice,
Is there a description of the algorithm somewhere? best regards, Dimiter Prodanov -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear Dimiter,
did you see the wiki page? http://fiji.sc/Ridge_Detection Cheers, Thorsten Am Dienstag, den 22.12.2015, 17:25 +0100 schrieb Dimiter Prodanov: > Dear Fabrice, > > Is there a description of the algorithm somewhere? > > best regards, > > Dimiter Prodanov > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Dear Thorsten,
I was not aware of this plugin. Thanks Dimiter On Tue, Dec 22, 2015 at 6:06 PM, Thorsten Wagner < [hidden email]> wrote: > Dear Dimiter, > > did you see the wiki page? > http://fiji.sc/Ridge_Detection > > Cheers, > Thorsten > > Am Dienstag, den 22.12.2015, 17:25 +0100 schrieb Dimiter Prodanov: > > Dear Fabrice, > > > > Is there a description of the algorithm somewhere? > > > > best regards, > > > > Dimiter Prodanov > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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