Not so easy ROIs determinations
Locked
Not so easy ROIs determinations
 
|
Dear all,
From the following picture : http://punias.free.fr/ImageJ/ring.tif I would like to extract automatically (i.e. by means of the use of a macro and/or plugin) the following ROI set: http://punias.free.fr/ImageJ/RoiSet.zip Does somebody have an idea on the best strategy to perform this? I thank you very much in advance for your help. My best regards, Philippe Philippe CARL Laboratoire de Biophotonique et Pharmacologie UMR 7213 CNRS - Université de Strasbourg Faculté de Pharmacie 74 route du Rhin 67401 ILLKIRCH Tel : +33(0)3 68 85 41 84 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Not so easy ROIs determinations
|
|
On Wednesday 30 Jul 2014 15:21:46 Philippe CARL wrote:
> From the following picture : > http://punias.free.fr/ImageJ/ring.tif > > I would like to extract automatically (i.e. by means of the use of a macro > and/or plugin) the following ROI set: Can I ask if you really need the ROI sets? Using binary regions (via the particle analyzer or particles8) is much easier and you can redirect measurements to any other images too. Cheers Gabriel -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
|
|
In reply to this post by CARL Philippe (LBP)
First: Threshold the objects
2nd: Analyse particles with storage in roi manager (without holes) 3rd: Loop over the found ROis: threshold with inverted background inside the actual ROI; apply Analyse particles; merge the actual roi with the found. ready Regards Karsten Am 30.07.2014 um 15:21 schrieb Philippe CARL <[hidden email]>: > Dear all, > > From the following picture : > > http://punias.free.fr/ImageJ/ring.tif > > I would like to extract automatically (i.e. by means of the use of a macro > and/or plugin) the following ROI set: > > http://punias.free.fr/ImageJ/RoiSet.zip > > Does somebody have an idea on the best strategy to perform this? > > I thank you very much in advance for your help. > > My best regards, > > Philippe > > > > Philippe CARL > > Laboratoire de Biophotonique et Pharmacologie > > UMR 7213 CNRS - Université de Strasbourg > > Faculté de Pharmacie > > 74 route du Rhin > > 67401 ILLKIRCH > > Tel : +33(0)3 68 85 41 84 > > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Not so easy ROIs determinations
|
|
In reply to this post by CARL Philippe (LBP)
Hi Philippe,
one possible solution might be a macro like the following: Threshold, Analyze particles, recording XStart, YStart to the Results table. run("Analyze Particles...", "display clear record"); Then iterate over the results Table. For each entry, call the Versatile Wand plugin with default options (i.e., 'record holes' should be unchecked) at XStart, YStart, and add to the ROI Manager. http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start Michael ________________________________________________________________ On Jul 30, 2014, at 15:21, Philippe CARL wrote: > Dear all, > > From the following picture : > > http://punias.free.fr/ImageJ/ring.tif > > I would like to extract automatically (i.e. by means of the use of a macro > and/or plugin) the following ROI set: > > http://punias.free.fr/ImageJ/RoiSet.zip > > Does somebody have an idea on the best strategy to perform this? > > I thank you very much in advance for your help. > > My best regards, > > Philippe > > > > Philippe CARL > > Laboratoire de Biophotonique et Pharmacologie > > UMR 7213 CNRS - Université de Strasbourg > > Faculté de Pharmacie > > 74 route du Rhin > > 67401 ILLKIRCH > > Tel : +33(0)3 68 85 41 84 > > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Not so easy ROIs determinations
|
|
Dear Michael,
Your proposed solution is indeed working, thanks a lot!!! Just a small remark about your plugin Website: the name of the macro on the Website should be "Versatile_Wand.java" and not "versatile_wand.java" which is giving a compilation error. I'm still in the process of studying all the other proposed solutions and thanks a lot for all the contributors. My best regards, Philippe -----Message d'origine----- De : ImageJ Interest Group [mailto:[hidden email]] De la part de Michael Schmid Envoyé : mercredi 30 juillet 2014 15:58 À : [hidden email] Objet : Re: Not so easy ROIs determinations Hi Philippe, one possible solution might be a macro like the following: Threshold, Analyze particles, recording XStart, YStart to the Results table. run("Analyze Particles...", "display clear record"); Then iterate over the results Table. For each entry, call the Versatile Wand plugin with default options (i.e., 'record holes' should be unchecked) at XStart, YStart, and add to the ROI Manager. http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:st art Michael ________________________________________________________________ On Jul 30, 2014, at 15:21, Philippe CARL wrote: > Dear all, > > From the following picture : > > http://punias.free.fr/ImageJ/ring.tif > > I would like to extract automatically (i.e. by means of the use of a > macro and/or plugin) the following ROI set: > > http://punias.free.fr/ImageJ/RoiSet.zip > > Does somebody have an idea on the best strategy to perform this? > > I thank you very much in advance for your help. > > My best regards, > > Philippe > > > > Philippe CARL > > Laboratoire de Biophotonique et Pharmacologie > > UMR 7213 CNRS - Université de Strasbourg > > Faculté de Pharmacie > > 74 route du Rhin > > 67401 ILLKIRCH > > Tel : +33(0)3 68 85 41 84 > > > > > -- > 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 |
Re: Not so easy ROIs determinations
|
|
Hi Philippe,
unfortunately, there is a limitation of the DokuWiki system used for the ImageJ Information and Documentation Portal (http://imagejdocu.tudor.lu/), where also the Versatile Wand is accessible: The names of uploaded files are always converted to lowercase. So I can't fix it, you have to rename it yourself. Michael ________________________________________________________________ On Jul 30, 2014, at 16:52, Philippe CARL wrote: > Dear Michael, > Your proposed solution is indeed working, thanks a lot!!! > Just a small remark about your plugin Website: the name of the macro on the > Website should be "Versatile_Wand.java" and not "versatile_wand.java" which > is giving a compilation error. > I'm still in the process of studying all the other proposed solutions and > thanks a lot for all the contributors. > My best regards, > Philippe > > -----Message d'origine----- > De : ImageJ Interest Group [mailto:[hidden email]] De la part de > Michael Schmid > Envoyé : mercredi 30 juillet 2014 15:58 > À : [hidden email] > Objet : Re: Not so easy ROIs determinations > > Hi Philippe, > > one possible solution might be a macro like the following: > > Threshold, Analyze particles, recording XStart, YStart to the Results table. > run("Analyze Particles...", "display clear record"); > > Then iterate over the results Table. For each entry, call the Versatile Wand > plugin with default options (i.e., 'record holes' should be unchecked) at > XStart, YStart, and add to the ROI Manager. > > http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:st > art > > > Michael > ________________________________________________________________ > On Jul 30, 2014, at 15:21, Philippe CARL wrote: > >> Dear all, >> >> From the following picture : >> >> http://punias.free.fr/ImageJ/ring.tif >> >> I would like to extract automatically (i.e. by means of the use of a >> macro and/or plugin) the following ROI set: >> >> http://punias.free.fr/ImageJ/RoiSet.zip >> >> Does somebody have an idea on the best strategy to perform this? >> >> I thank you very much in advance for your help. >> >> My best regards, >> >> Philippe >> >> >> >> Philippe CARL >> >> Laboratoire de Biophotonique et Pharmacologie >> >> UMR 7213 CNRS - Université de Strasbourg >> >> Faculté de Pharmacie >> >> 74 route du Rhin >> >> 67401 ILLKIRCH >> >> Tel : +33(0)3 68 85 41 84 >> >> >> >> >> -- >> 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 |
|
Hi Michael,
> So I can't fix it, you have to rename it yourself. Another option would be to migrate the documentation to the ImageJ Wiki instead (http://imagej.net/), which uses MediaWiki and has no such issues. Regards, Curtis On Wed, Jul 30, 2014 at 10:39 AM, Michael Schmid <[hidden email]> wrote: > Hi Philippe, > > unfortunately, there is a limitation of the DokuWiki system used for the > ImageJ Information and Documentation Portal (http://imagejdocu.tudor.lu/), > where also the Versatile Wand is accessible: > The names of uploaded files are always converted to lowercase. > > So I can't fix it, you have to rename it yourself. > > Michael > ________________________________________________________________ > On Jul 30, 2014, at 16:52, Philippe CARL wrote: > > > Dear Michael, > > Your proposed solution is indeed working, thanks a lot!!! > > Just a small remark about your plugin Website: the name of the macro on > the > > Website should be "Versatile_Wand.java" and not "versatile_wand.java" > which > > is giving a compilation error. > > I'm still in the process of studying all the other proposed solutions and > > thanks a lot for all the contributors. > > My best regards, > > Philippe > > > > -----Message d'origine----- > > De : ImageJ Interest Group [mailto:[hidden email]] De la part de > > Michael Schmid > > Envoyé : mercredi 30 juillet 2014 15:58 > > À : [hidden email] > > Objet : Re: Not so easy ROIs determinations > > > > Hi Philippe, > > > > one possible solution might be a macro like the following: > > > > Threshold, Analyze particles, recording XStart, YStart to the Results > table. > > run("Analyze Particles...", "display clear record"); > > > > Then iterate over the results Table. For each entry, call the Versatile > Wand > > plugin with default options (i.e., 'record holes' should be unchecked) at > > XStart, YStart, and add to the ROI Manager. > > > > > http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:st > > art > > > > > > Michael > > ________________________________________________________________ > > On Jul 30, 2014, at 15:21, Philippe CARL wrote: > > > >> Dear all, > >> > >> From the following picture : > >> > >> http://punias.free.fr/ImageJ/ring.tif > >> > >> I would like to extract automatically (i.e. by means of the use of a > >> macro and/or plugin) the following ROI set: > >> > >> http://punias.free.fr/ImageJ/RoiSet.zip > >> > >> Does somebody have an idea on the best strategy to perform this? > >> > >> I thank you very much in advance for your help. > >> > >> My best regards, > >> > >> Philippe > >> > >> > >> > >> Philippe CARL > >> > >> Laboratoire de Biophotonique et Pharmacologie > >> > >> UMR 7213 CNRS - Université de Strasbourg > >> > >> Faculté de Pharmacie > >> > >> 74 route du Rhin > >> > >> 67401 ILLKIRCH > >> > >> Tel : +33(0)3 68 85 41 84 > >> > >> > >> > >> > >> -- > >> 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 > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Not so easy ROIs determinations
|
|
In reply to this post by Michael Schmid
Hi Philippe,
by convention, Java class names should start with an uppercase character. Also ImageJ commands have names with uppercase first characters. That's why I wrote in the Usage/Installation instructions on the documentation wiki: Copy Versatile_Wand.java into the ImageJ plugins folder or a subfolder thereof. Make sure that you name the downloaded file ”Versatile_Wand.java”; uppercase/lowercase matters. --- On Jul 30, 2014, at 20:38, Curtis Rueden wrote: > Another option would be to migrate the documentation to the ImageJ Wiki > instead (http://imagej.net/), which uses MediaWiki and has no such issues. Hi Curtis, yes, we have a lot of ImageJ sites. Would be nice to have things in fewer places, and imagej.net might be a good one. Unfortunately it would be a lot of work to move everything there, unless this can be done by some automated process... Apart from the technical issues, I am not sure whether everyone will be happy about such a migration. These days, users in some countries might be unhappy having their account migrated from a European server to a server in the US (imagej.net seems to be hosted by the University of Wisconsin). Michael ________________________________________________________________ On Jul 31, 2014, at 09:12, Philippe CARL wrote: > Dear Michael, > For me to rename the file name is absolutely not an issue at all since I was > able to figure out the problem. > Nevertheless the question I asked yesterday was not for me but for a > colleague to whom I had then forwarded all the answers I had received. And > when he tried to compile your plugin he wasn't able to understand where the > problem comes from and how to fix it. > Thus if you are only able to save lowercase filenames within the DokuWiki > system, a solution to the problem could be to rename the class name to the > lowercase version within the plugin... > My best regards, > Philippe > > -----Message d'origine----- > De : ImageJ Interest Group [mailto:[hidden email]] De la part de > Michael Schmid > Envoyé : mercredi 30 juillet 2014 17:40 > À : [hidden email] > Objet : Re: Not so easy ROIs determinations > > Hi Philippe, > > unfortunately, there is a limitation of the DokuWiki system used for the > ImageJ Information and Documentation Portal (http://imagejdocu.tudor.lu/), > where also the Versatile Wand is accessible: > The names of uploaded files are always converted to lowercase. > > So I can't fix it, you have to rename it yourself. > > Michael > ________________________________________________________________ > On Jul 30, 2014, at 16:52, Philippe CARL wrote: > >> Dear Michael, >> Your proposed solution is indeed working, thanks a lot!!! >> Just a small remark about your plugin Website: the name of the macro >> on the Website should be "Versatile_Wand.java" and not >> "versatile_wand.java" which is giving a compilation error. >> I'm still in the process of studying all the other proposed solutions >> and thanks a lot for all the contributors. >> My best regards, >> Philippe >> >> -----Message d'origine----- >> De : ImageJ Interest Group [mailto:[hidden email]] De la part de >> Michael Schmid Envoyé : mercredi 30 juillet 2014 15:58 À : >> [hidden email] Objet : Re: Not so easy ROIs determinations >> >> Hi Philippe, >> >> one possible solution might be a macro like the following: >> >> Threshold, Analyze particles, recording XStart, YStart to the Results > table. >> run("Analyze Particles...", "display clear record"); >> >> Then iterate over the results Table. For each entry, call the >> Versatile Wand plugin with default options (i.e., 'record holes' >> should be unchecked) at XStart, YStart, and add to the ROI Manager. >> >> http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_w >> and:st >> art >> >> >> Michael >> ________________________________________________________________ >> On Jul 30, 2014, at 15:21, Philippe CARL wrote: >> >>> Dear all, >>> >>> From the following picture : >>> >>> http://punias.free.fr/ImageJ/ring.tif >>> >>> I would like to extract automatically (i.e. by means of the use of a >>> macro and/or plugin) the following ROI set: >>> >>> http://punias.free.fr/ImageJ/RoiSet.zip >>> >>> Does somebody have an idea on the best strategy to perform this? >>> >>> I thank you very much in advance for your help. >>> >>> My best regards, >>> >>> Philippe >>> >>> >>> >>> Philippe CARL >>> >>> Laboratoire de Biophotonique et Pharmacologie >>> >>> UMR 7213 CNRS - Université de Strasbourg >>> >>> Faculté de Pharmacie >>> >>> 74 route du Rhin >>> >>> 67401 ILLKIRCH >>> >>> Tel : +33(0)3 68 85 41 84 >>> >>> >>> >>> >>> -- >>> 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 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
|
|
Hi Michael,
> yes, we have a lot of ImageJ sites. Would be nice to have things in > fewer places, and imagej.net might be a good one. We are working very hard to set up imagej.net as the central place for community ImageJ documentation, plugins, development, etc. This has been one of the ImageJ2 project's goals from the beginning. We are very interested in resolving any obstacles you perceive there. > Unfortunately it would be a lot of work to move everything there, > unless this can be done by some automated process... Unifying the two wikis in an automated fashion is on our to-do list. It is something to coordinate with the Tudor site maintainers. We are partnering with Tudor to co-organize the next ImageJ conference, so I expect we will discuss how to resolve the dichotomy between the two wikis before the next conference. > Apart from the technical issues, I am not sure whether everyone will > be happy about such a migration. These days, users in some countries > might be unhappy having their account migrated from a European server > to a server in the US (imagej.net seems to be hosted by the University > of Wisconsin). I view that as a technical obstacle that can be solved by setting up worldwide mirrors, and having imagej.net automatically select the most appropriate one based on the user's location. Regards, Curtis On Thu, Jul 31, 2014 at 3:09 AM, Michael Schmid <[hidden email]> wrote: > Hi Philippe, > > by convention, Java class names should start with an uppercase character. > Also ImageJ commands have names with uppercase first characters. > > That's why I wrote in the Usage/Installation instructions on the > documentation wiki: > > Copy Versatile_Wand.java into the ImageJ plugins folder or a subfolder > thereof. Make sure that you name the downloaded file ”Versatile_Wand.java”; > uppercase/lowercase matters. > > --- > > On Jul 30, 2014, at 20:38, Curtis Rueden wrote: > > Another option would be to migrate the documentation to the ImageJ Wiki > > instead (http://imagej.net/), which uses MediaWiki and has no such > issues. > > Hi Curtis, > > yes, we have a lot of ImageJ sites. Would be nice to have things in fewer > places, and imagej.net might be a good one. Unfortunately it would be a > lot of work to move everything there, unless this can be done by some > automated process... > > Apart from the technical issues, I am not sure whether everyone will be > happy about such a migration. These days, users in some countries might be > unhappy having their account migrated from a European server to a server in > the US (imagej.net seems to be hosted by the University of Wisconsin). > > > Michael > ________________________________________________________________ > On Jul 31, 2014, at 09:12, Philippe CARL wrote: > > > Dear Michael, > > For me to rename the file name is absolutely not an issue at all since I > was > > able to figure out the problem. > > Nevertheless the question I asked yesterday was not for me but for a > > colleague to whom I had then forwarded all the answers I had received. > And > > when he tried to compile your plugin he wasn't able to understand where > the > > problem comes from and how to fix it. > > Thus if you are only able to save lowercase filenames within the DokuWiki > > system, a solution to the problem could be to rename the class name to > the > > lowercase version within the plugin... > > My best regards, > > Philippe > > > > -----Message d'origine----- > > De : ImageJ Interest Group [mailto:[hidden email]] De la part de > > Michael Schmid > > Envoyé : mercredi 30 juillet 2014 17:40 > > À : [hidden email] > > Objet : Re: Not so easy ROIs determinations > > > > Hi Philippe, > > > > unfortunately, there is a limitation of the DokuWiki system used for the > > ImageJ Information and Documentation Portal (http://imagejdocu.tudor.lu/ > ), > > where also the Versatile Wand is accessible: > > The names of uploaded files are always converted to lowercase. > > > > So I can't fix it, you have to rename it yourself. > > > > Michael > > ________________________________________________________________ > > On Jul 30, 2014, at 16:52, Philippe CARL wrote: > > > >> Dear Michael, > >> Your proposed solution is indeed working, thanks a lot!!! > >> Just a small remark about your plugin Website: the name of the macro > >> on the Website should be "Versatile_Wand.java" and not > >> "versatile_wand.java" which is giving a compilation error. > >> I'm still in the process of studying all the other proposed solutions > >> and thanks a lot for all the contributors. > >> My best regards, > >> Philippe > >> > >> -----Message d'origine----- > >> De : ImageJ Interest Group [mailto:[hidden email]] De la part de > >> Michael Schmid Envoyé : mercredi 30 juillet 2014 15:58 À : > >> [hidden email] Objet : Re: Not so easy ROIs determinations > >> > >> Hi Philippe, > >> > >> one possible solution might be a macro like the following: > >> > >> Threshold, Analyze particles, recording XStart, YStart to the Results > > table. > >> run("Analyze Particles...", "display clear record"); > >> > >> Then iterate over the results Table. For each entry, call the > >> Versatile Wand plugin with default options (i.e., 'record holes' > >> should be unchecked) at XStart, YStart, and add to the ROI Manager. > >> > >> http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_w > >> and:st > >> art > >> > >> > >> Michael > >> ________________________________________________________________ > >> On Jul 30, 2014, at 15:21, Philippe CARL wrote: > >> > >>> Dear all, > >>> > >>> From the following picture : > >>> > >>> http://punias.free.fr/ImageJ/ring.tif > >>> > >>> I would like to extract automatically (i.e. by means of the use of a > >>> macro and/or plugin) the following ROI set: > >>> > >>> http://punias.free.fr/ImageJ/RoiSet.zip > >>> > >>> Does somebody have an idea on the best strategy to perform this? > >>> > >>> I thank you very much in advance for your help. > >>> > >>> My best regards, > >>> > >>> Philippe > >>> > >>> > >>> > >>> Philippe CARL > >>> > >>> Laboratoire de Biophotonique et Pharmacologie > >>> > >>> UMR 7213 CNRS - Université de Strasbourg > >>> > >>> Faculté de Pharmacie > >>> > >>> 74 route du Rhin > >>> > >>> 67401 ILLKIRCH > >>> > >>> Tel : +33(0)3 68 85 41 84 > >>> > >>> > >>> > >>> > >>> -- > >>> 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 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
«
Return to ImageJ
|
1 view|%1 views
| Free forum by Nabble | Edit this page |