Visualize orthogonal views / 3D reconstruction

[lechristophe]

Dear all,

I have Zstacks (.tif format) that I would like to visualize as orthogonal
views and/or 3D reconstructions. I tried the ImageJ OrthView plugin but it
is very slow and buggy. Volume Viewer plugin is also quite slow. Do you
recommand any free software, preferably OSX or multi-platform, that can
handle thse task with a reasonnable performance  (I'm on an iMac Core2Duo
2.4 GHz, 2Go RAM). I tried BioImageXD but it is very unstable. I wanted to
try Osirix but I don't know if it handles .tif files and also it is OSX 10.5
only (I'm under 10.4).

Any other propositions ?

Christophe Leterrier

[Colin Poczatek]

One thing I've been playing around with is Visit from LLNL.
https://wci.llnl.gov/codes/visit/

It can open a stack of tifs from a image list file (ie a text file with
the path to each image), do an intensity volume plot, orthogonal
views/thresholds etc.

But, it's not simple/small software (it was written to render/visualize
terabyte sized datasets), and the UI isn't exactly intuitive.

I've run it on a Linux/Core2Duo and a OSX/G4 machine, so it's pretty
platform agnostic.

Hope that helped,
Collin



Quoting Christophe Leterrier <[hidden email]>:

> Dear all,
>
> I have Zstacks (.tif format) that I would like to visualize as orthogonal
> views and/or 3D reconstructions. I tried the ImageJ OrthView plugin but it
> is very slow and buggy. Volume Viewer plugin is also quite slow. Do you
> recommand any free software, preferably OSX or multi-platform, that can
> handle thse task with a reasonnable performance  (I'm on an iMac Core2Duo
> 2.4 GHz, 2Go RAM). I tried BioImageXD but it is very unstable. I wanted to
> try Osirix but I don't know if it handles .tif files and also it is OSX 10.5
> only (I'm under 10.4).
>
> Any other propositions ?
>
> Christophe Leterrier
>

The information transmitted in this electronic communication is intended only
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and/or privileged material. Any review, retransmission, dissemination or other
use of or taking of any action in reliance upon this information by persons or
entities other than the intended recipient is prohibited. If you received this
information in error, please contact the Compliance HelpLine at 800-856-1983 and
properly dispose of this information.

[Leon Espinosa]

Dear Christophe, osirix works ok with .tif stacks (saved from Imagej).  
I have found an old version that works with OS X 10.4

http://sourceforge.net/project/downloading.php?groupname=osirix&filename=OsiriX_Int275.zip&use_mirror=kent

you can contact me off line if you need help (in french... is ok !)

Leon

Le 2 avr. 08 à 14:48, Christophe Leterrier a écrit :

> Dear all,
>
> I have Zstacks (.tif format) that I would like to visualize as  
> orthogonal
> views and/or 3D reconstructions. I tried the ImageJ OrthView plugin  
> but it
> is very slow and buggy. Volume Viewer plugin is also quite slow. Do  
> you
> recommand any free software, preferably OSX or multi-platform, that  
> can
> handle thse task with a reasonnable performance  (I'm on an iMac  
> Core2Duo
> 2.4 GHz, 2Go RAM). I tried BioImageXD but it is very unstable. I  
> wanted to
> try Osirix but I don't know if it handles .tif files and also it is  
> OSX 10.5
> only (I'm under 10.4).
>
> Any other propositions ?
>
> Christophe Leterrier
>

Leon Espinosa
Laboratoire des Rickettsies du Pr. RAOULT
UMR CNRS 6020
Fac. de Medecine de la Timone
27 Bd Jean Moulin
13005 Marseille

tel  [phone]
fax [phone]

portable: 06 79 25 97 40

[NeLaS]

Christophe,

You could try Voxx2:

http://www.nephrology.iupui.edu/imaging/voxx/

I used it a few times to render TIF stacks and it worked well. It has a
function to cut planes so that might do the job for you.

bruno

On Wed, Apr 2, 2008 at 10:13 AM, Joseph Poczatek <
[hidden email]> wrote:

> One thing I've been playing around with is Visit from LLNL.
> https://wci.llnl.gov/codes/visit/
>
> It can open a stack of tifs from a image list file (ie a text file with
> the path to each image), do an intensity volume plot, orthogonal
> views/thresholds etc.
>
> But, it's not simple/small software (it was written to render/visualize
> terabyte sized datasets), and the UI isn't exactly intuitive.
>
> I've run it on a Linux/Core2Duo and a OSX/G4 machine, so it's pretty
> platform agnostic.
>
> Hope that helped,
> Collin
>
>
>
>
> Quoting Christophe Leterrier <[hidden email]>:
>
>  Dear all,
> >
> > I have Zstacks (.tif format) that I would like to visualize as
> > orthogonal
> > views and/or 3D reconstructions. I tried the ImageJ OrthView plugin but
> > it
> > is very slow and buggy. Volume Viewer plugin is also quite slow. Do you
> > recommand any free software, preferably OSX or multi-platform, that can
> > handle thse task with a reasonnable performance  (I'm on an iMac
> > Core2Duo
> > 2.4 GHz, 2Go RAM). I tried BioImageXD but it is very unstable. I wanted
> > to
> > try Osirix but I don't know if it handles .tif files and also it is OSX
> > 10.5
> > only (I'm under 10.4).
> >
> > Any other propositions ?
> >
> > Christophe Leterrier
> >
> >
>
>
>
> The information transmitted in this electronic communication is intended
> only
> for the person or entity to whom it is addressed and may contain
> confidential
> and/or privileged material. Any review, retransmission, dissemination or
> other
> use of or taking of any action in reliance upon this information by
> persons or
> entities other than the intended recipient is prohibited. If you received
> this
> information in error, please contact the Compliance HelpLine at
> 800-856-1983 and
> properly dispose of this information.
>

--
Bruno C. Vellutini
organelas.com | ccnelas.org | desertoresdaescada.com

Centro de Biologia Marinha (CEBIMar)
Universidade de São Paulo
Av. Manoel H. do Rego km 131,5
11600-000 São Sebastião, SP, Brasil
http://www.usp.br/cbm/

[Albert Cardona]

You can visualize orthoslices trivially with Bene Schmid's
ImageJ_3D_Viewer.jar plugin for ImageJ.
Requires java3d to be installed -which it is, by default, in macosx.

You can get a copy of of Bene's viewer in his webpage:

"http://132.187.25.13/home/?category=Download&page=Viewer3D

After installing it, just open a stack, launch the plugin, choose
orthoslices.
Use the hand tool to rotate in 3D space.
 From the menus you can bring up sliders to move the 3 planes along the
axes.

He also has a plugin that makes it dead-simple to install java3d in
non-macosx systems.

Albert

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

[Joel Sheffield]

Have you tried the ImageJ Stacks>reslice command?  You can set any
number of slices, and create  a "z" stack that is orthogonal to your
slice.  The trick is to enter the distance between adjacent slices.  

Joel



Date sent:       Wed, 2 Apr 2008 14:48:14 +0200
Send reply to:   ImageJ Interest Group <[hidden email]>
From:           Christophe Leterrier
<[hidden email]>
Subject:         Visualize orthogonal views / 3D reconstruction
To:             [hidden email]

> Dear all,
>
> I have Zstacks (.tif format) that I would like to visualize as orthogonal
> views and/or 3D reconstructions. I tried the ImageJ OrthView plugin but it
> is very slow and buggy. Volume Viewer plugin is also quite slow. Do you
> recommand any free software, preferably OSX or multi-platform, that can
> handle thse task with a reasonnable performance  (I'm on an iMac Core2Duo
> 2.4 GHz, 2Go RAM). I tried BioImageXD but it is very unstable. I wanted to
> try Osirix but I don't know if it handles .tif files and also it is OSX 10.5
> only (I'm under 10.4).
>
> Any other propositions ?
>
> Christophe Leterrier

--
Joel B. Sheffield, Ph.D.
Biology Department, Temple University
1900 North 12th Street
Philadelphia, PA 19122
[hidden email]  
[phone], fax [phone]
http://astro.temple.edu/~jbs

[Gabriel Landini]

On Wednesday 02 April 2008 15:09:41 Albert Cardona wrote:
 
> He also has a plugin that makes it dead-simple to install java3d in
> non-macosx systems.

What if I want to install the java 3d in local user installation of the jdk?
(it is asking me for a system-wise install).

Cheers,

G.

[dscho]

Hi,

On Wed, 2 Apr 2008, Gabriel Landini wrote:

> On Wednesday 02 April 2008 15:09:41 Albert Cardona wrote:
>  
> > He also has a plugin that makes it dead-simple to install java3d in
> > non-macosx systems.
>
> What if I want to install the java 3d in local user installation of the
> jdk? (it is asking me for a system-wise install).

That is a slightly bigger problem.  You can install the files in a
directory of your choice, but you have to pass
"-Djava.ext.dirs=/the/path/to/the/jars/and/jnilibs/" to java.

Hth,
Dscho

[Jonathan Jackson-2]

On Wed, 2 Apr 2008 10:09:41 -0400, Albert Cardona
<[hidden email]> wrote:

>You can visualize orthoslices trivially with Bene Schmid's
>ImageJ_3D_Viewer.jar plugin for ImageJ.
>Requires java3d to be installed -which it is, by default, in macosx.
>
>You can get a copy of of Bene's viewer in his webpage:
>
>"http://132.187.25.13/home/?category=Download&page=Viewer3D
>
>After installing it, just open a stack, launch the plugin, choose
>orthoslices.
>Use the hand tool to rotate in 3D space.
> From the menus you can bring up sliders to move the 3 planes along the
>axes.
>

I tried this plugin, and get the message:
"Java 3D Error: Off screen rendering not supported by this setup. Falling
back to screen capturing"
and and I get a new window with zero width. Has anyone seen this before?

I'm using a linux system (FC5/x86_64) with NVidia graphics card and
proprietary driver.  The example file Java3Dexample.jar works perfectly.

Jon

[Gabriel Landini]

On Friday 04 April 2008 09:51:17 Jonathan Jackson wrote:

> I tried this plugin, and get the message:
> "Java 3D Error: Off screen rendering not supported by this setup. Falling
> back to screen capturing"
> and and I get a new window with zero width. Has anyone seen this before?

I also have a problem with that plugin. It shows a long and narrow viewer
window (no errors reported, though) .

I am using suse linux, Nvidia dual monitor.

I already let the author know about this.

G.

[Benjamin Schmid-2]

Hi,

On Fri, Apr 4, 2008 at 11:34 AM, Gabriel Landini <[hidden email]>
wrote:

> On Friday 04 April 2008 09:51:17 Jonathan Jackson wrote:
>
> > I tried this plugin, and get the message:
> > "Java 3D Error: Off screen rendering not supported by this setup.
> Falling
> > back to screen capturing"
>

This is a warning which shows up on many systems. It tells you that
offscreen
rendering is not supported by the graphics card. Some functions of the
viewer,
which would need this capability, use screen captures in this case, so it's
possible to work with it. If you are annoyed by the error message, edit
ImageJ's
run script by passing -Dj3d.noOffScreen=true to the java call
(something like  java -Xmx1000m  -Dj3d.noOffScreen=true  ...)


>
> > and and I get a new window with zero width. Has anyone seen this before?
>


> I also have a problem with that plugin. It shows a long and narrow viewer
> window (no errors reported, though) .
>
> I am using suse linux, Nvidia dual monitor.
>
> I already let the author know about this.
>
>
I just included a workaround from Albert Cardona and uploaded a new version
of
the viewer. Unfortunately, I can't test it on my machine since I haven't had
this
problem before. So maybe you could do that for me ;-)

Best wishes,

Benjamin

[Gabriel Landini]

On Friday 04 April 2008 11:36:29 Benjamin Schmid wrote:
> I just included a workaround from Albert Cardona and uploaded a new version
> of
> the viewer. Unfortunately, I can't test it on my machine since I haven't
> had this
> problem before. So maybe you could do that for me ;-)

Still I get a narrow and tall viewer window.
I also get this warning when using the 3d-example-stack.tif or any other
stack.

***** polygon with only one vertex?! *****

Regards

Gabriel

[Mathieu Goeminne]

Hi all,

I try to use ImageJ to blur an image using the API (not the GUI) with a
3x3 convolution matrix gaussian blur. So I use a GaussianBlur object,
and call the blur(ImagePlus, double) method. Comparing the result with
that is obtained using the ImageJ GUI or the GIMP, it appears my call
make an "excessive" blur : for a given sigma (the standard deviation),
"my" blurring is stronger that the Gimp or the ImageJ GUI blurring.

An other problem seems to be an artificial minimum on the sigma : for
every sigma < 1, the result seems to be
Approximately the same as  a sigma=1 blurring. For instance, a sigma=0
blurring blurs really my image, but it should return a non-modified image.

The documentation (and the API) of ImageJ says :

> 'Radius' means the radius of decay to exp(-0.5) ~ 61%, i.e. the
standard deviation sigma of the Gaussian (this is the same as in
Photoshop, but different from the previous ImageJ function 'Gaussian
Blur', where a value 2.5 times as much has to be entered)

I tried to divide my sigma by 2.5, but there is no visible difference,
and the sigma=0 case is not resolved.

I use ImageJ 1.38

Any idea?

Thanks.

[Jonathan Jackson-2]

On Fri, 4 Apr 2008 11:52:21 +0100, Gabriel Landini <[hidden email]> wrote:

>On Friday 04 April 2008 11:36:29 Benjamin Schmid wrote:
>> I just included a workaround from Albert Cardona and uploaded a new version
>> of
>> the viewer. Unfortunately, I can't test it on my machine since I haven't
>> had this
>> problem before. So maybe you could do that for me ;-)
>
>Still I get a narrow and tall viewer window.
>I also get this warning when using the 3d-example-stack.tif or any other
>stack.
>
>***** polygon with only one vertex?! *****
>

Likewise, I get a narrow, tall viewer window.  Interestingly the zoom and
hand tools do manipulate the image if you can click on it (1 pixel wide.)

The "Off screen rendering not supported" message has gone away with the new
version.

Cheers,
Jon

[Leon Espinosa]

Hello I have the same "off screen" error message with a G5 ppc Mac OS  
X 10.5, and with "surface" option it crashs with message:


java.lang.IllegalArgumentException:TriangleArray: illegal vertexCount
     at javax.media.j3d.TriangleArray.<init>(TriangleArray.java:119)
     at  
com
.sun
.j3d.utils.geometry.GeometryInfo.getGeometryArray(GeometryInfo.java:
2557)
     at javax.media.j3d.Font3D.triangulateGlyphs(Font3D.java:402)
     at  
javax.media.j3d.Text3DRetained.updateCharacterData(Text3DRetained.java:
684)
     at javax.media.j3d.Text3DRetained.setString(Text3DRetained.java:
234)
     at javax.media.j3d.Text3D.<init>(Text3D.java:243)
     at ij3d.CoordinateSystem.addText(CoordinateSystem.java:66)
     at ij3d.CoordinateSystem.<init>(CoordinateSystem.java:51)
     at ij3d.Content.createBoundingBox(Content.java:90)
     at isosurface.MeshGroup.calculateMinMaxCenterPoint(MeshGroup.java:
102)
     at isosurface.MeshGroup.<init>(MeshGroup.java:61)
     at ij3d.Image3DUniverse.addMesh(Image3DUniverse.java:199)
     at isosurface.MeshGroup.addContent(MeshGroup.java:177)
     at ij3d.ImageJ3DViewer.run(ImageJ3DViewer.java:48)
     at  
ij
.plugin
.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:243)
     at  
ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:102)
     at ij.IJ.runUserPlugIn(IJ.java:160)
     at ij.IJ.runPlugIn(IJ.java:124)
     at ij.Executer.runCommand(Executer.java:104)
     at ij.Executer.run(Executer.java:58)
     at java.lang.Thread.run(Thread.java:613)


The java 3D test with cubes works fine...

Any ideas ?

Thanks, Leon




Le 4 avr. 08 à 12:36, Benjamin Schmid a écrit :

> Hi,
>
> On Fri, Apr 4, 2008 at 11:34 AM, Gabriel Landini  
> <[hidden email]>
> wrote:
>
>> On Friday 04 April 2008 09:51:17 Jonathan Jackson wrote:
>>
>>> I tried this plugin, and get the message:
>>> "Java 3D Error: Off screen rendering not supported by this setup.
>> Falling
>>> back to screen capturing"
>>
>
> This is a warning which shows up on many systems. It tells you that
> offscreen
> rendering is not supported by the graphics card. Some functions of the
> viewer,
> which would need this capability, use screen captures in this case,  
> so it's
> possible to work with it. If you are annoyed by the error message,  
> edit
> ImageJ's
> run script by passing -Dj3d.noOffScreen=true to the java call
> (something like  java -Xmx1000m  -Dj3d.noOffScreen=true  ...)
>
>
>>
>>> and and I get a new window with zero width. Has anyone seen this  
>>> before?
>>
>
>
>> I also have a problem with that plugin. It shows a long and narrow  
>> viewer
>> window (no errors reported, though) .
>>
>> I am using suse linux, Nvidia dual monitor.
>>
>> I already let the author know about this.
>>
>>
> I just included a workaround from Albert Cardona and uploaded a new  
> version
> of
> the viewer. Unfortunately, I can't test it on my machine since I  
> haven't had
> this
> problem before. So maybe you could do that for me ;-)
>
> Best wishes,
>
> Benjamin
>

Leon Espinosa
Laboratoire des Rickettsies du Pr. RAOULT
UMR CNRS 6020
Fac. de Medecine de la Timone
27 Bd Jean Moulin
13005 Marseille

tel  [phone]
fax [phone]

portable: 06 79 25 97 40

[Gabriel Landini]

On Friday 04 April 2008 12:40:48 Mathieu Goeminne wrote:
> I use ImageJ 1.38

Does this also happen is the most recent version 1.40c?

G.

[Albert Cardona]

> Likewise, I get a narrow, tall viewer window.  Interestingly the zoom and
> hand tools do manipulate the image if you can click on it (1 pixel wide.)
>  


I suspect there is a thread synchronization issue with the Canvas3D.
We are working on a work-around.

If you select the 3D window, and open the jython interpreter, call:

win = WindowManager.getCurrentWindow()
from java.awt import Dimension
win.setMinimumSize(Dimension(512,512))


you will see that the window is no longer a vertical slit.

More on this soon.

Albert

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

[Albert Cardona]

Hi Leon,

I have a patch for the Text3D Exception problem, I forgot to commit it.
Thanks for reminding me.

Albert

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

[Jan Stuehmer]

Hi Mathieu,

have you tried a bigger convolution kernel than 3x3 ?
A higher sigma than half the size of the convolution kernel makes not much
sense if you want to have a reasonable precision.

To adjust the kernel size ( m x m ) to the sigma value you can compute
the value
of the normal distribution (normalized gaussian) for x = 0.5 * m
This gives you a hint of the error you get if you discretize the normal
distribution
for that filter size.

What is a normal distribution with sigma=0 ? It should be the Dirac measure
which should result in a non-modified image, you are right. But this is
a special
case of the normal distribution.
In the end it depends on how ImageJ computes it's filter kernel because
you get
a division by zero if sigma is zero.

Cheers,
Jan

Mathieu Goeminne schrieb:

> Hi all,
>
> I try to use ImageJ to blur an image using the API (not the GUI) with a
> 3x3 convolution matrix gaussian blur. So I use a GaussianBlur object,
> and call the blur(ImagePlus, double) method. Comparing the result with
> that is obtained using the ImageJ GUI or the GIMP, it appears my call
> make an "excessive" blur : for a given sigma (the standard deviation),
> "my" blurring is stronger that the Gimp or the ImageJ GUI blurring.
>
> An other problem seems to be an artificial minimum on the sigma : for
> every sigma < 1, the result seems to be
> Approximately the same as  a sigma=1 blurring. For instance, a sigma=0
> blurring blurs really my image, but it should return a non-modified
> image.
>
> The documentation (and the API) of ImageJ says :
>
>  
>> 'Radius' means the radius of decay to exp(-0.5) ~ 61%, i.e. the
>>    
> standard deviation sigma of the Gaussian (this is the same as in
> Photoshop, but different from the previous ImageJ function 'Gaussian
> Blur', where a value 2.5 times as much has to be entered)
>
> I tried to divide my sigma by 2.5, but there is no visible difference,
> and the sigma=0 case is not resolved.
>
> I use ImageJ 1.38
>
> Any idea?
>
> Thanks.
>
>  

[Michael Schmid]

Hi Mathieu,

the following PlugIn gets the same result as the gui Process>Filters>
Gaussian Blur command with ImageJ 1.40c (also for sigma = 0; small
deviations may arise form different accurracy; I have set it rather
low here with 0.01):

import ij.plugin.filter.GaussianBlur;
import ij.plugin.PlugIn;
import ij.process.*;
import ij.gui.*;
import ij.*;

public class TestGaussian implements PlugIn {

     double sigma = 1; //or 0 or whatever you like

     public void run(String unusedArg) {
         ImagePlus imp = IJ.getImage();
         if (imp==null) return;
         ImageProcessor ip = imp.getProcessor();
         ip.setRoi((Roi)null); //otherwise, a snapshot would be needed
         GaussianBlur gb = new GaussianBlur();
         gb.blurGaussian(ip, sigma, sigma, 0.01);
         imp.updateAndDraw();
     }
}

----
Note that the inner workings of Gaussian Blur have changed in
versions 1.38r, 1.38s and 1.38u, so the current API will not
fit the pre-1.38u versions.
---
Using the built-in Gaussian Blur is *much* faster that using
convolution with a (m x m) Gaussian kernel and also faster than
successive convolution operations with (m x 1) and (1 x m)
Gaussian kernels (especially for large sigma).

Michael
________________________________________________________________

On 6 Apr 2008, at 17:22, Jan Stühmer wrote:

> Hi Mathieu,
>
> have you tried a bigger convolution kernel than 3x3 ?
> A higher sigma than half the size of the convolution kernel makes  
> not much
> sense if you want to have a reasonable precision.
>
> To adjust the kernel size ( m x m ) to the sigma value you can  
> compute the value
> of the normal distribution (normalized gaussian) for x = 0.5 * m
> This gives you a hint of the error you get if you discretize the  
> normal distribution
> for that filter size.
>
> What is a normal distribution with sigma=0 ? It should be the Dirac  
> measure
> which should result in a non-modified image, you are right. But  
> this is a special
> case of the normal distribution.
> In the end it depends on how ImageJ computes it's filter kernel  
> because you get
> a division by zero if sigma is zero.
>
> Cheers,
> Jan
>
> Mathieu Goeminne schrieb:
>> Hi all,
>>
>> I try to use ImageJ to blur an image using the API (not the GUI)  
>> with a
>> 3x3 convolution matrix gaussian blur. So I use a GaussianBlur object,
>> and call the blur(ImagePlus, double) method. Comparing the result  
>> with
>> that is obtained using the ImageJ GUI or the GIMP, it appears my call
>> make an "excessive" blur : for a given sigma (the standard  
>> deviation),
>> "my" blurring is stronger that the Gimp or the ImageJ GUI blurring.
>>
>> An other problem seems to be an artificial minimum on the sigma : for
>> every sigma < 1, the result seems to be
>> Approximately the same as  a sigma=1 blurring. For instance, a  
>> sigma=0
>> blurring blurs really my image, but it should return a non-
>> modified image.
>>
>> The documentation (and the API) of ImageJ says :
>>
>>
>>> 'Radius' means the radius of decay to exp(-0.5) ~ 61%, i.e. the
>>>
>> standard deviation sigma of the Gaussian (this is the same as in
>> Photoshop, but different from the previous ImageJ function 'Gaussian
>> Blur', where a value 2.5 times as much has to be entered)
>>
>> I tried to divide my sigma by 2.5, but there is no visible  
>> difference,
>> and the sigma=0 case is not resolved.
>>
>> I use ImageJ 1.38
>>
>> Any idea?
>>
>> Thanks.
>>
>>