ImageJ plugin for 3D visualization and distance measurement
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Shalin Mehta |
ImageJ plugin for 3D visualization and distance measurement
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Hi All,
Is there a plugin for ImageJ that will allow 3D visualization and allow the visualization to be annotated with some measurements (at least distance between two points)? Thanks Shalin
On Sat, Mar 1, 2008 at 1:33 PM, Nishigandha Naik <[hidden email]> wrote: If your files are in the format, pic, tiff, jpg, bmp, -- ~~~~~~~~~~~~~~~~~~~~~~~~~ Shalin Mehta mobile: +65-90694182 blog: shalin.wordpress.com ~~~~~~~~~~~~~~~~~~~~~~~~~~ Bioimaging Lab, Block-E3A, #7-10 Div of Bioengineering, NUS Singapore 117574 website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html Liver Cancer Functional Genomics Lab, #6-05 National Cancer Centre, Singapore 169610 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ What is light? ''Light behaves like Voltaire, the French genius, 250 years ago. He was born as a conservative Catholic, he lived as a liberal Protestant, and he returned to Catholicism when he faced the end of his life. Light is born as photons. It travels through space as a wave, and it dies finally as a photon.'' - Einstein as quoted in Lohmann's paper (JOSA-A, Vol. 17, No.10, pp.1755-1762) |
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Haberman, Ann |
Re: ImageJ plugin for batch conversions
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Hello list!
Since we are talking about ImageJ plugins, does anyone know of a
plugin that will automate the renaming of files in batch conversions
of entire folders. I would love to be able to "record" a
series of actions on an image, and then apply those same actions to
all the images in a folder - much like the "record actions"
function in Photoshop.
That would be a major time saver!
Ann
Hi All, On Sat, Mar 1, 2008 at 1:33 PM, Nishigandha Naik <[hidden email]> wrote: -- Ann Haberman, PhD Department of Laboratory Medicine Yale University School of Medicine 1 Gilbert St. TAC S541 New Haven, CT 06510 203-785-7349 203-785-5415 (fax) [hidden email] |
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lechristophe |
Re: ImageJ plugin for batch conversions
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In reply to this post by Shalin Mehta
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Have a look at the multiple image processor :
http://ciar.rcm.upr.edu/projects/imageprocessor/multiples Christophe Leterrier
On Mon, Mar 3, 2008 at 5:43 PM, Ann Haberman <[hidden email]> wrote: Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal |
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G. Esteban Fernandez |
Re: ImageJ plugin for batch conversions
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In reply to this post by Shalin Mehta
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi Ann, Below is a simple macro that will parse through all the images in a directory, apply 'actions', and overwrite the image using the same filename. To preserve the original files make copies of the folders before applying this. If you want to save the processed images with a different filename it's a little more involved, contact me off list for help with that. Hope this helps. Esteban dir = getDirectory("Choose a Directory "); list = getFileList(dir); setBatchMode(true); // to not open images in window, runs up to 6 times faster for (i=0; i<list.length; i++) { path = dir + list[i]; open(path); // INSERT RECORDED ACTIONS HERE run("Save"); } On Mon, Mar 3, 2008 at 10:43 AM, Ann Haberman <[hidden email]> wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Hello list! > > Since we are talking about ImageJ plugins, does anyone know of a plugin that > will automate the renaming of files in batch conversions of entire folders. > I would love to be able to "record" a series of actions on an image, and > then apply those same actions to all the images in a folder - much like the > "record actions" function in Photoshop. > > That would be a major time saver! > Ann > > Hi All, > > Is there a plugin for ImageJ that will allow 3D visualization and allow the > visualization to be annotated with some measurements (at least distance > between two points)? > > Thanks > Shalin > On Sat, Mar 1, 2008 at 1:33 PM, Nishigandha Naik > <[hidden email]> wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > Hi > If your files are in the format, pic, tiff, jpg, bmp, > avi,mtg or jif, then you may try using free software > 'confoal assistant'. 'lsm' format cannot be seen. > Viewing of single or Z-section images, construction of > 3D and merging of images is possible. > Best wishes, > Nishigandha Naik > > -- > > > Ann Haberman, PhD > Department of Laboratory Medicine > Yale University School of Medicine > 1 Gilbert St. > TAC S541 > New Haven, CT 06510 > > 203-785-7349 > 203-785-5415 (fax) > [hidden email] > -- G. Esteban Fernandez, Ph.D. Associate Director Molecular Cytology Research Core Facility University of Missouri 1201 E. Rollins St. Columbia, MO 65211 573-882-4895 573-884-9676 fax http://www.biotech.missouri.edu/mcc/ |
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Haberman, Ann |
Re: ImageJ plugin for batch conversions
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In reply to this post by lechristophe
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Hi Christophe,
How does one generate the macro that will be applied?
thanks!
Ann
Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Have a look at the multiple image processor : On Mon, Mar 3, 2008 at 5:43 PM, Ann Haberman <[hidden email]> wrote: -- Ann Haberman, PhD Department of Laboratory Medicine Yale University School of Medicine 1 Gilbert St. TAC S541 New Haven, CT 06510 203-785-7349 203-785-5415 (fax) [hidden email] |
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Richard Harris-6 |
Re: ImageJ plugin for batch conversions
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In reply to this post by Haberman, Ann
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Or you could just get Irfanview (free download) as it has this
capability as part of the basic system Rick, From: Confocal Microscopy
List [mailto:[hidden email]] On Behalf Of Ann Haberman Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hello list! Since we are talking about ImageJ plugins, does anyone know
of a plugin that will automate the renaming of files in batch conversions of
entire folders. I would love to be able to "record" a series of
actions on an image, and then apply those same actions to all the images in a
folder - much like the "record actions" function in Photoshop. That would be a major time saver! Ann
--
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lechristophe |
Re: ImageJ plugin for batch conversions
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In reply to this post by lechristophe
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
I think you can just record a series of commands using the macro recorder (it is built-in in ImageJ, have a look at the help on IJ's website) and export the commands as a macro .txt file and point to it in the multiple plugin.
On Mon, Mar 3, 2008 at 6:10 PM, Ann Haberman <[hidden email]> wrote:
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Rosemary.White |
Re: ImageJ plugin for batch conversions
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In reply to this post by Richard Harris-6
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
go to something like www.tucows.com Rosemary Rosemary White [hidden email] CSIRO Plant Industry ph. 61 (0)2-6246 5475 GPO Box 1600 fax. 61 (0)2-6246 5334 Canberra, ACT 2601 Australia On 4/3/08 4:13 AM, "Richard Harris" <[hidden email]> wrote: Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal |
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Batch file rename can be easilly done also in Total commander. There is really usefull renaming tool ;-) using also masks so you can rename only parts of the name or add indexing. Anything you want.
Best wishes.
-----Original Message-----
I’d put in another vote for
Irfanview, very easy batch file renaming and even changing formats, etc. Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Hi All, If your files are in the format, pic, tiff, jpg, bmp,
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Reece, Jeff (NIH/NIEHS) [V] |
Re: ImageJ plugin for batch conversions
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In reply to this post by Shalin Mehta
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal If you just want to rename files, a good utility for that purpose is Renamer: http://www.snapfiles.com/get/denrenamer.html Cheers, Jeff -----Original Message----- From: Ann Haberman [mailto:[hidden email]] Sent: Monday, March 03, 2008 11:43 AM To: [hidden email] Subject: Re: ImageJ plugin for batch conversions ---------------------- Information from the mail header ----------------------- Sender: Confocal Microscopy List <[hidden email]> Poster: Ann Haberman <[hidden email]> Subject: Re: ImageJ plugin for batch conversions ------------------------------------------------------------------------ ------- --============_-1007559894==_ma============ Content-Type: text/plain; charset="us-ascii" ; format="flowed" Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hello list! Since we are talking about ImageJ plugins, does anyone know of a plugin that will automate the renaming of files in batch conversions of entire folders. I would love to be able to "record" a series of actions on an image, and then apply those same actions to all the images in a folder - much like the "record actions" function in Photoshop. That would be a major time saver! Ann >Hi All, > > Is there a plugin for ImageJ that will allow 3D visualization and >allow the visualization to be annotated with some measurements (at >least distance between two points)? > >Thanks >Shalin > >On Sat, Mar 1, 2008 at 1:33 PM, Nishigandha Naik ><<mailto:[hidden email]>[hidden email]> >wrote: > >Search the CONFOCAL archive at ><http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal>http://listser > >Hi > >If your files are in the format, pic, tiff, jpg, bmp, >avi,mtg or jif, then you may try using free software >'confoal assistant'. 'lsm' format cannot be seen. >Viewing of single or Z-section images, construction of >3D and merging of images is possible. >Best wishes, >Nishigandha Naik -- Ann Haberman, PhD Department of Laboratory Medicine Yale University School of Medicine 1 Gilbert St. TAC S541 New Haven, CT 06510 203-785-7349 203-785-5415 (fax) [hidden email] --============_-1007559894==_ma============ Content-Type: text/html; charset="us-ascii" Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal <!doctype html public "-//W3C//DTD W3 HTML//EN"> <html><head><style type="text/css"><!-- blockquote, dl, ul, ol, li { padding-top: 0 ; padding-bottom: 0 } --></style><title>Re: ImageJ plugin for batch conversions</title></head><body> <div><br></div> <div>Hello list!</div> <div><br></div> <div>Since we are talking about ImageJ plugins, does anyone know of a plugin that will automate the renaming of files in batch conversions of entire folders. I would love to be able to "record" a series of actions on an image, and then apply those same actions to all the images in a folder - much like the "record actions" function in Photoshop.</div> <div><br></div> <div>That would be a major time saver!</div> <div>Ann</div> <div><br></div> <blockquote type="cite" cite>Hi All,<br> <br> Is there a plugin for ImageJ that will allow 3D visualization and allow the visualization to be annotated with some measurements (at least distance between two points)?<br> <br> Thanks<br> Shalin<br> </blockquote> <blockquote type="cite" cite>On Sat, Mar 1, 2008 at 1:33 PM, Nishigandha Naik <<a href="mailto:[hidden email]">[hidden email]</a >> wrote:<br> <blockquote>Search the CONFOCAL archive at<br> <a href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal" >http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal</a><br> <br> Hi<br> </blockquote> <blockquote>If your files are in the format, pic, tiff, jpg, bmp,<br> avi,mtg or jif, then you may try using free software<br> 'confoal assistant'. 'lsm' format cannot be seen.<br> Viewing of single or Z-section images, construction of<br> 3D and merging of images is possible.<br> Best wishes,</blockquote> <blockquote>Nishigandha Naik</blockquote> </blockquote> <div><br></div> <x-sigsep><pre>-- </pre></x-sigsep> <div><br> Ann Haberman, PhD<br> Department of Laboratory Medicine<br> Yale University School of Medicine<br> 1 Gilbert St.<br> TAC S541<br> New Haven, CT 06510<br> <br> 203-785-7349<br> 203-785-5415 (fax)<br> [hidden email]<br> </div> </body> </html> --============_-1007559894==_ma============-- |
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Dr. Mark A. DeCoster |
Re: ImageJ plugin for batch conversions-Irfanview
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In reply to this post by Schebique
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
We also use Irfanview, for example to be able to easily view
high resolution Tiff files captured in Metamorph which are not viewable in your
typical windows “preview” (“drawing failed”, etc.). Dr. Mark A. DeCoster Associate Professor Biomedical Engineering Louisiana Tech University http://www2.latech.edu/~decoster/ -----Original
Message----- I’d put in another vote for
Irfanview, very easy batch file renaming and even changing formats, etc. Search
the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Hi
All, If
your files are in the format, pic, tiff, jpg, bmp,
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