ImageJ

Local Thickness for anisotropic voxels

_‹ Previous Topic Next Topic _›

Classic

List

Threaded

6 messages Options

Ofra Golani

Local Thickness for anisotropic voxels

Hi,

Does the Local Thickness plugin assume isotropic voxels (voxel size is equal in all directions) ?
Is there any plugin available for calculating 3D local thickness for anisotropic voxels ?

Thanks

Ofra

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Thomas Boudier-3

Re: Local Thickness for anisotropic voxels

Dear Ofra,

I do not think there is a plugin for local thickness for anisotropic
voxels. I can suggest you to have a look to 3D distance map that may
give you the information you want, or simply make your image anisotropic :

getVoxelSize(width, height, depth, unit);
run("Reslice [/]...", "output=&width start=Top");
run("Reslice [/]...", "output=&width start=Top");

Best,

Thomas

On 30/09/2015 06:44, Ofra Golani wrote:

> Hi,
>
> Does the Local Thickness plugin assume isotropic voxels (voxel size is equal in all directions) ?
> Is there any plugin available for calculating 3D local thickness for anisotropic voxels ?
>
> Thanks
>
> Ofra
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> --
> /***************************************************************/
> Thomas Boudier, Associate Professor, UPMC,
> Université Pierre et Marie Curie, Paris, France.
> BioInformatics Institute (BII)/IPAL, Singapore.
> /**************************************************************/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Michael Doube-4

Re: Local Thickness for anisotropic voxels

Hi Ofra,

To reiterate what Thomas said, the Local Thickness algorithm does indeed assume isotropically-spaced pixels and image resampling into an isotropic space may help you. BoneJ's implementation of Local Thickness warns you if your pixels are anisotropic (often the case in confocal microscopy and CT imaging).

Michael

On 30/09/15 02:03, Thomas Boudier wrote:

> Dear Ofra,
>
> I do not think there is a plugin for local thickness for anisotropic
> voxels. I can suggest you to have a look to 3D distance map that may
> give you the information you want, or simply make your image anisotropic :
>
> getVoxelSize(width, height, depth, unit);
> run("Reslice [/]...", "output=&width start=Top");
> run("Reslice [/]...", "output=&width start=Top");
>
> Best,
>
> Thomas
>
> On 30/09/2015 06:44, Ofra Golani wrote:
>> Hi,
>>
>> Does the Local Thickness plugin assume isotropic voxels (voxel size is equal in all directions) ?
>> Is there any plugin available for calculating 3D local thickness for anisotropic voxels ?
>>
>> Thanks
>>
>> Ofra
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
>> --
>> /***************************************************************/
>> Thomas Boudier, Associate Professor, UPMC,
>> Université Pierre et Marie Curie, Paris, France.
>> BioInformatics Institute (BII)/IPAL, Singapore.
>> /**************************************************************/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

[http://www.rvc.ac.uk/media/default/images/social-media/change.gif]

[RVC Logo - link to RVC Website]<http://www.rvc.ac.uk> [Twitter icon - link to RVC (Official) Twitter] <http://twitter.com/RoyalVetCollege> [Facebook icon - link to RVC (Official) Facebook] <http://www.facebook.com/theRVC> [YouTube icon - link to RVC YouTube] <http://www.youtube.com/user/RoyalVetsLondon?feature=mhee> [Pinterest icon - link to RVC Pinterest] <http://pinterest.com/royalvetcollege/> [Instagram icon - link to RVC Instagram] <http://instagram.com/royalvetcollege>

This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College (RVC). If you are not the intended recipient, please notify the sender and be advised that you have received this message in error and that any use, dissemination, forwarding, printing, or copying is strictly prohibited. Unless stated expressly in this email, this email does not create, form part of, or vary any contractual or unilateral obligation. Email communication cannot be guaranteed to be secure or error free as information could be intercepted, corrupted, amended, lost, destroyed, incomplete or contain viruses. Therefore, we do not accept liability for any such matters or their consequences. Communication with us by email will be taken as acceptance of the risks inherent in doing so.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Ofra Golani

Re: Local Thickness for anisotropic voxels

In reply to this post by Ofra Golani

Thanks Thomas,

Making my stack isotropic is a good idea.
However, I have image with voxel size 0.08*0.08*0.24 um, shouldn't I use TransformJ scale instead of Reslice
I think the best would be to get image with 3 times the number of slices and voxel size 0.08*0.08*0.08.

Thanks
Ofra

-----Original Message-----
From: Thomas Boudier [mailto:[hidden email]]
Sent: Wednesday, September 30, 2015 4:00 AM
Subject: Re: Local Thickness for anisotropic voxels

Dear Ofra,

I do not think there is a plugin for local thickness for anisotropic voxels. I can suggest you to have a look to 3D distance map that may give you the information you want, or simply make your image anisotropic :

getVoxelSize(width, height, depth, unit); run("Reslice [/]...", "output=&width start=Top"); run("Reslice [/]...", "output=&width start=Top");

Best,

Thomas

On 30/09/2015 06:44, Ofra Golani wrote:

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Thomas Boudier-3

Re: Local Thickness for anisotropic voxels

Hi Ofra,

Yes, you're right, you can also use scale from Image/Scale or
TransformJ. TransformJ offers more interpolation options but both
functions should give quite similar results.

Best,

Thomas

On 01/10/2015 05:00, Ofra Golani wrote:

> Thanks Thomas,
>
> Making my stack isotropic is a good idea.
> However, I have image with voxel size 0.08*0.08*0.24 um, shouldn't I use TransformJ scale instead of Reslice
> I think the best would be to get image with 3 times the number of slices and voxel size 0.08*0.08*0.08.
>
> Thanks
> Ofra
>
> -----Original Message-----
> From: Thomas Boudier [mailto:[hidden email]]
> Sent: Wednesday, September 30, 2015 4:00 AM
> Subject: Re: Local Thickness for anisotropic voxels
>
> Dear Ofra,
>
> I do not think there is a plugin for local thickness for anisotropic voxels. I can suggest you to have a look to 3D distance map that may give you the information you want, or simply make your image anisotropic :
>
> getVoxelSize(width, height, depth, unit); run("Reslice [/]...", "output=&width start=Top"); run("Reslice [/]...", "output=&width start=Top");
>
> Best,
>
> Thomas
>
> On 30/09/2015 06:44, Ofra Golani wrote:
>> Hi,
>>
>> Does the Local Thickness plugin assume isotropic voxels (voxel size is equal in all directions) ?
>> Is there any plugin available for calculating 3D local thickness for anisotropic voxels ?
>>
>> Thanks
>>
>> Ofra
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
>> --
>> /***************************************************************/
>> Thomas Boudier, Associate Professor, UPMC,
>> Université Pierre et Marie Curie, Paris, France.
>> BioInformatics Institute (BII)/IPAL, Singapore.
>> /**************************************************************/
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
/***************************************************************/
Thomas Boudier, Associate Professor, UPMC,
Université Pierre et Marie Curie, Paris, France.
BioInformatics Institute (BII)/IPAL, Singapore.
/**************************************************************/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Shameem Sampath

Re: Local Thickness for anisotropic voxels

In reply to this post by Michael Doube-4

Hi Michael,
Is there any guidance available on how to do image resampling into an isotropic space for a series of Dicon images from a CT scan of a human knee?
Regards,
Shameem Sampath

Confidentiality Notice: This e-mail and any attachments are intended solely for the addressee and may contain confidential or privileged information. If you are not the named addressee, or the person responsible for delivering the message to the named addressee, please notify the sender as soon as possible and delete the material from your computer. This message will be protected by copyright. If it has come to you in error, you must not take any action based on its contents nor must you copy or show the message to any person other than the intended recipient.
The Bluespot Knee Clinic

> On 30 Sep 2015, at 11:28, Doube, Michael <[hidden email]> wrote:
>
> Hi Ofra,
>
> To reiterate what Thomas said, the Local Thickness algorithm does indeed assume isotropically-spaced pixels and image resampling into an isotropic space may help you. BoneJ's implementation of Local Thickness warns you if your pixels are anisotropic (often the case in confocal microscopy and CT imaging).
>
> Michael
>
>> On 30/09/15 02:03, Thomas Boudier wrote:
>> Dear Ofra,
>>
>> I do not think there is a plugin for local thickness for anisotropic
>> voxels. I can suggest you to have a look to 3D distance map that may
>> give you the information you want, or simply make your image anisotropic :
>>
>> getVoxelSize(width, height, depth, unit);
>> run("Reslice [/]...", "output=&width start=Top");
>> run("Reslice [/]...", "output=&width start=Top");
>>
>> Best,
>>
>> Thomas
>>
>>> On 30/09/2015 06:44, Ofra Golani wrote:
>>> Hi,
>>>
>>> Does the Local Thickness plugin assume isotropic voxels (voxel size is equal in all directions) ?
>>> Is there any plugin available for calculating 3D local thickness for anisotropic voxels ?
>>>
>>> Thanks
>>>
>>> Ofra
>>>
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>>
>>> --
>>> /***************************************************************/
>>> Thomas Boudier, Associate Professor, UPMC,
>>> Université Pierre et Marie Curie, Paris, France.
>>> BioInformatics Institute (BII)/IPAL, Singapore.
>>> /**************************************************************/
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> [http://www.rvc.ac.uk/media/default/images/social-media/change.gif]
>
> [RVC Logo - link to RVC Website]<http://www.rvc.ac.uk> [Twitter icon - link to RVC (Official) Twitter] <http://twitter.com/RoyalVetCollege> [Facebook icon - link to RVC (Official) Facebook] <http://www.facebook.com/theRVC> [YouTube icon - link to RVC YouTube] <http://www.youtube.com/user/RoyalVetsLondon?feature=mhee> [Pinterest icon - link to RVC Pinterest] <http://pinterest.com/royalvetcollege/> [Instagram icon - link to RVC Instagram] <http://instagram.com/royalvetcollege>
>
> This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College (RVC). If you are not the intended recipient, please notify the sender and be advised that you have received this message in error and that any use, dissemination, forwarding, printing, or copying is strictly prohibited. Unless stated expressly in this email, this email does not create, form part of, or vary any contractual or unilateral obligation. Email communication cannot be guaranteed to be secure or error free as information could be intercepted, corrupted, amended, lost, destroyed, incomplete or contain viruses. Therefore, we do not accept liability for any such matters or their consequences. Communication with us by email will be taken as acceptance of the risks inherent in doing so.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html