measuring length of fibers

[Hartley, William H.]

Hey All,
I am trying to figure out a way to measure length of multiple fibers on one image.  I have tried thresholding but the fiber wont get completely thresholded (particle analyzer wont be accurate).  So as for now I have been doing each fiber individually which is very time consuming... 60 fibers per image x 30 images x 10 trials... you get the picture.  Is there a better way to do this.. i have attached an image for inspection.

Thanks
Bill

[Patrick Pirrotte]

Hi all,

I just released a IJUpdate, an ImageJ updater which can be found here:
http://imagejdocu.tudor.lu/imagej-documenation-wiki/plugins/ijupdate

IJUpdate_ is an updater for ImageJ. It supports both stable (1.36b at the
time of writing) and testing (1.37q at the time of writing). It connects to
an ImageJ update server which contains a list of all the ImageJ releases
(currently this  update server is set to image-archive.org but another url
can be specified). The update server runs a script which sends back a list
of available versions and an url to the update files (all on the NIH ImageJ
site).

IMPORTANT NOTICE: The plugin is in beta stadium. It has been tested on
Windows XP, MacOS and Linux.As the update server has to reflect the newest
ImageJ version for testing. Right now I still have to manually reflect the
newest version on the update server. This should change in the near future.

These features has been implemented:

    * switching between testing and stable version
    * expert mode: ability to downgrade /upgrade freely between different
stable versions. (useful for developers who want to test their plugins under
different ImageJ versions.)
    * proxy settings recognized (no auth yet, only host/port combination)
    * rollback feature if upgrade/downgrade fails.

I would suggest NOT to use the plugin in a productive environment yet. As
the plugin involves overwriting a running ImageJ it would be nice if a few
ImageJ developpers would try it out and send me their thoughts on how to
improve the plugin.

I'd like to add a plugin update feature (for plugins registered with a
defined versioning), macro updating etc...

Best regards,

Patrick

[Patrick Pirrotte]

Hi again,

I've updated my script on the update server based on an idea I implemented
from Jérôme's latest macro. I don't need to update the version string on a
weekly basis anymore at every new testing version. I'd like to add that the
actual jar or zip is still donwloaded from the ImageJ website. You can check
this by pointing your browsers to
www.image-archive.org?ijupdate.php?type=stable and
www.image-archive.org?ijupdate.phptype=testing. Both IJ version and download
url are shown.

Patrick


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Patrick Pirrotte
Sent: 01 September 2006 11:11
To: [hidden email]
Subject: IJUpdate


Hi all,

I just released a IJUpdate, an ImageJ updater which can be found here:
http://imagejdocu.tudor.lu/imagej-documenation-wiki/plugins/ijupdate

IJUpdate_ is an updater for ImageJ. It supports both stable (1.36b at the
time of writing) and testing (1.37q at the time of writing). It connects to
an ImageJ update server which contains a list of all the ImageJ releases
(currently this  update server is set to image-archive.org but another url
can be specified). The update server runs a script which sends back a list
of available versions and an url to the update files (all on the NIH ImageJ
site).

IMPORTANT NOTICE: The plugin is in beta stadium. It has been tested on
Windows XP, MacOS and Linux.As the update server has to reflect the newest
ImageJ version for testing. Right now I still have to manually reflect the
newest version on the update server. This should change in the near future.

These features has been implemented:

    * switching between testing and stable version
    * expert mode: ability to downgrade /upgrade freely between different
stable versions. (useful for developers who want to test their plugins under
different ImageJ versions.)
    * proxy settings recognized (no auth yet, only host/port combination)
    * rollback feature if upgrade/downgrade fails.

I would suggest NOT to use the plugin in a productive environment yet. As
the plugin involves overwriting a running ImageJ it would be nice if a few
ImageJ developpers would try it out and send me their thoughts on how to
improve the plugin.

I'd like to add a plugin update feature (for plugins registered with a
defined versioning), macro updating etc...

Best regards,

Patrick

[Corentin Cras-Méneur-2]

On 01 sept. 2006, at 11:11, Patrick Pirrotte wrote:

> Hi all,
>

        Hi Patrick,

> I just released a IJUpdate, an ImageJ updater which can be found here:
> http://imagejdocu.tudor.lu/imagej-documenation-wiki/plugins/ijupdate


This looks like a very nice plugin indeed!!!
I just tested it under MacOS X (10.4.7 - ij 1.37m). It properly  
detected the latest testing version (1.37q), but failed to install it  
("error during file copy").
I thought you'd want to know.
Cheers,


                Corentin

[Patrick Pirrotte]

Sorry, I tried to do 3 things at the same time.

The urls should be www.image-archive.org/ijupdate.php?type=stable and
www.image-archive.org/ijupdate.php?type=testing

Patrick

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Patrick Pirrotte
Sent: 01 September 2006 11:55
To: [hidden email]
Subject: Re: IJUpdate


Hi again,

I've updated my script on the update server based on an idea I implemented
from Jérôme's latest macro. I don't need to update the version string on a
weekly basis anymore at every new testing version. I'd like to add that the
actual jar or zip is still donwloaded from the ImageJ website. You can check
this by pointing your browsers to
www.image-archive.org?ijupdate.php?type=stable and
www.image-archive.org?ijupdate.phptype=testing. Both IJ version and download
url are shown.

Patrick


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Patrick Pirrotte
Sent: 01 September 2006 11:11
To: [hidden email]
Subject: IJUpdate


Hi all,

I just released a IJUpdate, an ImageJ updater which can be found here:
http://imagejdocu.tudor.lu/imagej-documenation-wiki/plugins/ijupdate

IJUpdate_ is an updater for ImageJ. It supports both stable (1.36b at the
time of writing) and testing (1.37q at the time of writing). It connects to
an ImageJ update server which contains a list of all the ImageJ releases
(currently this  update server is set to image-archive.org but another url
can be specified). The update server runs a script which sends back a list
of available versions and an url to the update files (all on the NIH ImageJ
site).

IMPORTANT NOTICE: The plugin is in beta stadium. It has been tested on
Windows XP, MacOS and Linux.As the update server has to reflect the newest
ImageJ version for testing. Right now I still have to manually reflect the
newest version on the update server. This should change in the near future.

These features has been implemented:

    * switching between testing and stable version
    * expert mode: ability to downgrade /upgrade freely between different
stable versions. (useful for developers who want to test their plugins under
different ImageJ versions.)
    * proxy settings recognized (no auth yet, only host/port combination)
    * rollback feature if upgrade/downgrade fails.

I would suggest NOT to use the plugin in a productive environment yet. As
the plugin involves overwriting a running ImageJ it would be nice if a few
ImageJ developpers would try it out and send me their thoughts on how to
improve the plugin.

I'd like to add a plugin update feature (for plugins registered with a
defined versioning), macro updating etc...

Best regards,

Patrick

[Dimiter Prodanov]

>Hi,

I think there was a stereological approach to estimate the fiber length.
But in any way it is not by individually outlining fibers.
Check this resource for a primer
http://www.disector.com/neuroscience-publications.htm
and
  http://www.ehponline.org/members/1999/107p367-375rogers/rogers-full.html

best regards


_______________________________________________________________________
Dr Dimiter Prodanov, MD, Ph.D.

Neural Engineering Rehabilitation Laboratory
(Laboratoire de Génie de la Réhabilitation Neurale)
Département de Physiologie et Pharmacologie
Université catholique de Louvain
Avenue Hippocrate, 54
POBox UCL-5446 / B-1200 Bruxelles -Belgique-
Phone: [phone]
Fax: [phone]

http://www.md.ucl.ac.be/gren

[Gabriel Landini]

On Friday 01 September 2006 11:19, Patrick Pirrotte wrote:
> I've updated my script on the update server based on an idea I implemented
> from Jérôme's latest macro.

Hi Patrick, this is interesting.

Why does the plugin have to connect to a 3rd party update server
(www.image-archive.org) instead of handling the information directly between
the client and wayne's site?

Some suggestions:
make the option to also download the source and expand it in the ImageJ
directory
make an option to download the functions.html page into the ImageJ directory
make an option to download the notes.html page into the ImageJ directory
make an option to download the daily build

[Arne Seitz-2]

Dear all,

I just finished two plugins which handle PerkinElmer raw files (PerkinElmer
Imaging Suite, RELEASE Date Feb. 21 2006). The parameters (e.g. number of
channels, number of slices, number of time points) of the image series are
read from the cfg file. The raw-files are then automatically imported into a
stack and afterwards converted to an Image5D stack (plugin from Joachim
Walter).

The Plugins + a short description can be found under:

http://www.embl-heidelberg.de/ExternalInfo/almf/htdocs/almf_website/html/PE_
Plugins.htm

Best regards
Arne

____________________________________________________
 
Arne Seitz, Scientific Officer
Advanced Light Microscopy Facility
EMBL Heidelberg
 
[phone]

[Patrick Pirrotte]

Hi all,

In the next version, IJUpdate will connect directly to the NIH server for a
valid IJ list.

Could you please output the content of the system console (err) which should
contain java specific error messages?

Best regards,

Patrick

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Corentin Cras-Méneur
Sent: 01 September 2006 12:14
To: [hidden email]
Subject: Re: IJUpdate


On 01 sept. 2006, at 11:11, Patrick Pirrotte wrote:

> Hi all,
>

        Hi Patrick,

> I just released a IJUpdate, an ImageJ updater which can be found here:
> http://imagejdocu.tudor.lu/imagej-documenation-wiki/plugins/ijupdate


This looks like a very nice plugin indeed!!!
I just tested it under MacOS X (10.4.7 - ij 1.37m). It properly  
detected the latest testing version (1.37q), but failed to install it  
("error during file copy").
I thought you'd want to know.
Cheers,


                Corentin

[Corentin Cras-Méneur-2]

On 05 sept. 2006, at 10:22, Patrick Pirrotte wrote:

> Hi all,
>
> In the next version, IJUpdate will connect directly to the NIH  
> server for a
> valid IJ list.
>
> Could you please output the content of the system console (err)  
> which should
> contain java specific error messages?

Sorry for the very late reply, but I was away (and I still am  
actually ;-) ).
It appears that the location the updater attempts to update is not  
valid. I get:
IOException:/Volumes/GriGris/Applications/Data/BioInf/ImageJ/ij.jar  
(No such file or directory)

The ij.jar has no reason to be in this folder. On MacOS X it is  
located inside the application-package.
The proper location in this very case should be:
/Volumes/GriGris/Applications/Data/BioInf/ImageJ/ImageJ.app/Contents/
Resources/Java/ij.jar


Corentin

[jmutterer]

Corentin, you should reinstall a recent version of ImageJ for MacOsX.
With the new version, the ij.jar file is now located outside of the
application package, in the ImageJ folder. This should fix the
problem.

Jerome


On 9/9/06, Corentin Cras-Méneur <[hidden email]> wrote:

> On 05 sept. 2006, at 10:22, Patrick Pirrotte wrote:
>
> > Hi all,
> >
> > In the next version, IJUpdate will connect directly to the NIH
> > server for a
> > valid IJ list.
> >
> > Could you please output the content of the system console (err)
> > which should
> > contain java specific error messages?
>
> Sorry for the very late reply, but I was away (and I still am
> actually ;-) ).
> It appears that the location the updater attempts to update is not
> valid. I get:
> IOException:/Volumes/GriGris/Applications/Data/BioInf/ImageJ/ij.jar
> (No such file or directory)
>
> The ij.jar has no reason to be in this folder. On MacOS X it is
> located inside the application-package.
> The proper location in this very case should be:
> /Volumes/GriGris/Applications/Data/BioInf/ImageJ/ImageJ.app/Contents/
> Resources/Java/ij.jar
>
>
> Corentin
>

[Patrick Pirrotte]

Hi Corentin,

As Jérôme suggested, the quick solution for you may be to install a
current ImageJ version first and from then on IJUpdate should work. I
don't have a Mac, which makes debugging for that platform quite tedious.
I'm using ImageJ's getHomedir method to get the directory containing
ij.jar. I'll check if there have been variations of this in previous
ImageJ versions.

Nevertheless I hope to make IJUpdate fully compatible to ImageJ version 1.33
and above (version 1.33 was released two years ago). Fully compatible means allowing upgrades and downgrades using IJUpdate dialogs. The problem is that ImageJ has changed a lot and I need to time travel into ImageJ's old source code. Going below 1.33 is probably unrealistic and a waste of effort.

Best regards,

Patrick----- Original Message -----From: jerome mutterer Date: Saturday, September 9, 2006 13:34Subject: Re: IJUpdateTo: [hidden email]> Corentin, you should reinstall a recent version of ImageJ for MacOsX.> With the new version, the ij.jar file is now located outside of the> application package, in the ImageJ folder. This should fix the> problem.> > Jerome> > > On 9/9/06, Corentin Cras-Méneur  wrote:> > On 05 sept. 2006, at 10:22, Patrick Pirrotte wrote:> >> > > Hi all,> > >> > > In the next version, IJUpdate will connect directly to the NIH> > > server for a> > > valid IJ list.> > >> > > Could you please output the content of the system console (err)> > > which should> > > contain java specific error messages?> >> > Sorry for the very late reply, but I was away (and I still am> > actually ;-) ).> > It appears that the location the updater attempts to update is not> > valid. I get:> > IOException:/Volumes/GriGris/Applications/Data/BioInf/ImageJ/ij.jar> > (No such file or directory)> >> > The ij.jar has no reason to be in this folder. On MacOS X it is> > located inside the application-package.> > The proper location in this very case should be:> > > /Volumes/GriGris/Applications/Data/BioInf/ImageJ/ImageJ.app/Contents/> Resources/Java/ij.jar> >> >> > Corentin> >>

[Corentin Cras-Méneur-2]

On 09 sept. 2006, at 12:11, Patrick Pirrotte wrote:

> Hi Corentin,
>

        Hi Patrick,

As I mentioned in my reply to Jérôme, I was away for a while and  
again, I apologize for taking so long to follow-up on this issue,


> As Jérôme suggested, the quick solution for you may be to install a
> current ImageJ version first and from then on IJUpdate should work. I
> don't have a Mac, which makes debugging for that platform quite  
> tedious.
> I'm using ImageJ's getHomedir method to get the directory containing
> ij.jar. I'll check if there have been variations of this in previous
> ImageJ versions.

That was indeed the problem. I had a previous install of the core  
application which required the ij.jar to be embedded in the app itself  
instead of being in the application folder.

>
> Nevertheless I hope to make IJUpdate fully compatible to ImageJ  
> version 1.33
> and above (version 1.33 was released two years ago). Fully  
> compatible means allowing upgrades and downgrades using IJUpdate  
> dialogs. The problem is that ImageJ has changed a lot and I need to  
> time travel into ImageJ's old source code. Going below 1.33 is  
> probably unrealistic and a waste of effort.
>

Installing the 1.36 version of the core application entirely corrects  
the problem.
Thanks a million for all your help,


Corentin

[Corentin Cras-Méneur-2]

    My deepest apologies for not following up before, but I was away  
for quite a while :-\

On 09 sept. 2006, at 5:36, jerome mutterer wrote:

> Corentin, you should reinstall a recent version of ImageJ for MacOsX.
> With the new version, the ij.jar file is now located outside of the
> application package, in the ImageJ folder. This should fix the
> problem.


Thanks a million for your suggestion. I followed your advice and it  
corrected the problem immediately of course. Thanks again,


Corentin