Visualization and Analysis of 3D Microscopic Images

classic Classic list List threaded Threaded
12 messages Options
Reply | Threaded
Open this post in threaded view
|

Visualization and Analysis of 3D Microscopic Images

Jeff Ellis
I am interested in using Slicer to generate 3D volumetric sculptural representations of histological structures (both normal and abnormal) found on light microscopy.

I've installed the software, as well as SlicerPathology module, and reviewed some training videos on youtube by Erich Breme (Thank you for that!)

I've also watched some training videos by Dr. Belevich, which were impressive....but I am left with questions on how to get started.


I hope to cut through a block of tissue embedded in paraffin and take digital images of the light microscopy slides as I thinly section the block.  I would then like to highlight the cells on each slide that I am interested in (i.e. Nerve cells) so that I can visualize their patterns and courses in 3d with a tool like slicer.org.   Hopefully SlicerPathology will help to make that task easy and accurate.

1.  Any advice on how best to scan the slides initially?  Format to use?  Is there a nomenclature to use when saving the images so the software understands the order of the slides?  Do I simply save .jpg files and number them 1.jpg 2.jpg 3.jpg etc and upload the folder with all??

2. Any advice on how to "line up" one slide to the next?  Or does the program do this for us?  These (unlike an MRI scan) will be hand mounted on glass slices, and may need digital alignment from one slide to the next??

3. Any thoughts on the appropriate step thickness through the tissue block?  How many slides to make? Or if there is a limit I should try to stay under?

Any practical advice would be most helpful. I apologize if these are all very basic questions, but I could not find any documentation or sample slide sets to help be better understand how to best approach this.

Looking forward to your thoughts. 

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Visualization and Analysis of 3D Microscopic Images

Andrey Fedorov-2
I am not an expert in digital pathology, but I can give you some
answers based on my understanding. I also cc the team behind
SlicerPathology so they can provide more guidance hopefully.

>
> 1.  Any advice on how best to scan the slides initially?  Format to use?  Is
> there a nomenclature to use when saving the images so the software
> understands the order of the slides?  Do I simply save .jpg files and number
> them 1.jpg 2.jpg 3.jpg etc and upload the folder with all??
>

The format most likely be determined by the scanner and software.
Quite often those scanners use proprietary formats, which are not
compatible with 3D Slicer, and you may need to use additional tools
for conversion (such as OpenSlide http://openslide.org/). The
resulting images may be too large to interact with using Slicer.

> 2. Any advice on how to "line up" one slide to the next?  Or does the
> program do this for us?  These (unlike an MRI scan) will be hand mounted on
> glass slices, and may need digital alignment from one slide to the next??
>

Slicer does not have custom tools to help with this task. You can load
individual sections and use Slicer Transform module to align them, but
you may be able to find more customized tools for this task. Someone
mentioned to me TrakEM2 for this task:
http://www.ini.uzh.ch/~acardona/trakem2.html, but I have not tried it
myself.

At this time, SlicerPathology can help you with segmenting cell nuclei
in (relatively) small patches of digital pathology images. The input
images should be in one of the non-proprietary formats that can be
read by Slicer (such as gif, tiff, or jpg).

> 3. Any thoughts on the appropriate step thickness through the tissue block?
> How many slides to make? Or if there is a limit I should try to stay under?
>

I don't have relevant practical experience to give you advice on this
one... I think for the most part this will be limited by the resources
you have to process the volume of the thin sections you will be
collecting.

> Any practical advice would be most helpful. I apologize if these are all
> very basic questions, but I could not find any documentation or sample slide
> sets to help be better understand how to best approach this.
>
> Looking forward to your thoughts.
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with
> unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Visualization and Analysis of 3D Microscopic Images

Andras Lasso-2
Aaron Ward's group worked a lot on reconstructing 3D volume from histology images slices (and registering to MRI volumes). They tried many different methods to register slices to each other, but finally ended up using strand-shaped fiducials. See for example this paper:
http://onlinelibrary.wiley.com/doi/10.1002/jmri.23767/abstract

In Slicer you can use the Fiducial registration wizard module (in SlicerIGT extension) to register slides to each other based on marked fiducial positions. Once you have the alignment transform, you would need to use the Resample volume module to resample the aligned slice on a common grid, and save the slice to file. Once you've registered all the slides, you can load the sequence of images as a volume (you just have to assign file names that have consecutive numbering, for example slide01.nrrd, slide02,nrrd, slide03.nrrd, ...). Once you have verified that this approach works, you can write scripts to automate the process.

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Andrey Fedorov
Sent: February 14, 2017 13:07
To: Jeff Ellis <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Saltz, Joel <[hidden email]>; Bremer, Erich <[hidden email]>
Subject: Re: [slicer-users] Visualization and Analysis of 3D Microscopic Images

I am not an expert in digital pathology, but I can give you some answers based on my understanding. I also cc the team behind SlicerPathology so they can provide more guidance hopefully.

>
> 1.  Any advice on how best to scan the slides initially?  Format to
> use?  Is there a nomenclature to use when saving the images so the
> software understands the order of the slides?  Do I simply save .jpg
> files and number them 1.jpg 2.jpg 3.jpg etc and upload the folder with all??
>

The format most likely be determined by the scanner and software.
Quite often those scanners use proprietary formats, which are not compatible with 3D Slicer, and you may need to use additional tools for conversion (such as OpenSlide http://openslide.org/). The resulting images may be too large to interact with using Slicer.

> 2. Any advice on how to "line up" one slide to the next?  Or does the
> program do this for us?  These (unlike an MRI scan) will be hand
> mounted on glass slices, and may need digital alignment from one slide to the next??
>

Slicer does not have custom tools to help with this task. You can load individual sections and use Slicer Transform module to align them, but you may be able to find more customized tools for this task. Someone mentioned to me TrakEM2 for this task:
http://www.ini.uzh.ch/~acardona/trakem2.html, but I have not tried it myself.

At this time, SlicerPathology can help you with segmenting cell nuclei in (relatively) small patches of digital pathology images. The input images should be in one of the non-proprietary formats that can be read by Slicer (such as gif, tiff, or jpg).

> 3. Any thoughts on the appropriate step thickness through the tissue block?
> How many slides to make? Or if there is a limit I should try to stay under?
>

I don't have relevant practical experience to give you advice on this one... I think for the most part this will be limited by the resources you have to process the volume of the thin sections you will be collecting.

> Any practical advice would be most helpful. I apologize if these are
> all very basic questions, but I could not find any documentation or
> sample slide sets to help be better understand how to best approach this.
>
> Looking forward to your thoughts.
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Visualization and Analysis of 3D Microscopic Images

Andrey Fedorov-2
In reply to this post by Andrey Fedorov-2
Andras, I believe the main purpose of the strands was to facilitate MRI to pathology registration. If MRI registration is not the objective, the process does not necessarily need to be that involved. (and even if it is - applicability of this approach for organs other than prostate remains to be demonstrated)

Don't get me wrong, Ward et al is a great approach for the specific task, and for someone with a lot of resources, but we should not overcomplicate the problem without necessity.

On Feb 14, 2017 18:19, "Andras Lasso" <[hidden email]> wrote:
Aaron Ward's group worked a lot on reconstructing 3D volume from histology images slices (and registering to MRI volumes). They tried many different methods to register slices to each other, but finally ended up using strand-shaped fiducials. See for example this paper:
http://onlinelibrary.wiley.com/doi/10.1002/jmri.23767/abstract

In Slicer you can use the Fiducial registration wizard module (in SlicerIGT extension) to register slides to each other based on marked fiducial positions. Once you have the alignment transform, you would need to use the Resample volume module to resample the aligned slice on a common grid, and save the slice to file. Once you've registered all the slides, you can load the sequence of images as a volume (you just have to assign file names that have consecutive numbering, for example slide01.nrrd, slide02,nrrd, slide03.nrrd, ...). Once you have verified that this approach works, you can write scripts to automate the process.

Andras

-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Andrey Fedorov
Sent: February 14, 2017 13:07
To: Jeff Ellis <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Saltz, Joel <[hidden email]>; Bremer, Erich <[hidden email]>
Subject: Re: [slicer-users] Visualization and Analysis of 3D Microscopic Images

I am not an expert in digital pathology, but I can give you some answers based on my understanding. I also cc the team behind SlicerPathology so they can provide more guidance hopefully.

>
> 1.  Any advice on how best to scan the slides initially?  Format to
> use?  Is there a nomenclature to use when saving the images so the
> software understands the order of the slides?  Do I simply save .jpg
> files and number them 1.jpg 2.jpg 3.jpg etc and upload the folder with all??
>

The format most likely be determined by the scanner and software.
Quite often those scanners use proprietary formats, which are not compatible with 3D Slicer, and you may need to use additional tools for conversion (such as OpenSlide http://openslide.org/). The resulting images may be too large to interact with using Slicer.

> 2. Any advice on how to "line up" one slide to the next?  Or does the
> program do this for us?  These (unlike an MRI scan) will be hand
> mounted on glass slices, and may need digital alignment from one slide to the next??
>

Slicer does not have custom tools to help with this task. You can load individual sections and use Slicer Transform module to align them, but you may be able to find more customized tools for this task. Someone mentioned to me TrakEM2 for this task:
http://www.ini.uzh.ch/~acardona/trakem2.html, but I have not tried it myself.

At this time, SlicerPathology can help you with segmenting cell nuclei in (relatively) small patches of digital pathology images. The input images should be in one of the non-proprietary formats that can be read by Slicer (such as gif, tiff, or jpg).

> 3. Any thoughts on the appropriate step thickness through the tissue block?
> How many slides to make? Or if there is a limit I should try to stay under?
>

I don't have relevant practical experience to give you advice on this one... I think for the most part this will be limited by the resources you have to process the volume of the thin sections you will be collecting.

> Any practical advice would be most helpful. I apologize if these are
> all very basic questions, but I could not find any documentation or
> sample slide sets to help be better understand how to best approach this.
>
> Looking forward to your thoughts.
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Fal

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Visualization and Analysis of 3D Microscopic Images

Andras Lasso-2
In reply to this post by Andrey Fedorov-2

Unless you can set up imaging that provides perfectly aligned histology image slices, you’ll need retrospective alignment. There is probably no simpler way of aligning images than using landmarks. Of course you need to have clearly identifiable landmarks, so you may have to add those, if there are no good inherent landmarks in the images.

 

Visual alignment is quick and easy if you only have translation, but if you also have rotation and potentially slight deformations, then it takes a lot of iterations to find good alignment. Landmark registration is very simple and predictable and can easily handle translation, rotation, and even deformation.

 

Andras

 

From: Andrey Fedorov [mailto:[hidden email]]
Sent: February 14, 2017 23:06
To: Andras Lasso <[hidden email]>
Cc: [hidden email]; Bremer, Erich <[hidden email]>; Saltz, Joel <[hidden email]>; Jeff Ellis <[hidden email]>
Subject: RE: [slicer-users] Visualization and Analysis of 3D Microscopic Images

 

Andras, I believe the main purpose of the strands was to facilitate MRI to pathology registration. If MRI registration is not the objective, the process does not necessarily need to be that involved. (and even if it is - applicability of this approach for organs other than prostate remains to be demonstrated)

 

Don't get me wrong, Ward et al is a great approach for the specific task, and for someone with a lot of resources, but we should not overcomplicate the problem without necessity.

 

On Feb 14, 2017 18:19, "Andras Lasso" <[hidden email]> wrote:

Aaron Ward's group worked a lot on reconstructing 3D volume from histology images slices (and registering to MRI volumes). They tried many different methods to register slices to each other, but finally ended up using strand-shaped fiducials. See for example this paper:
http://onlinelibrary.wiley.com/doi/10.1002/jmri.23767/abstract

In Slicer you can use the Fiducial registration wizard module (in SlicerIGT extension) to register slides to each other based on marked fiducial positions. Once you have the alignment transform, you would need to use the Resample volume module to resample the aligned slice on a common grid, and save the slice to file. Once you've registered all the slides, you can load the sequence of images as a volume (you just have to assign file names that have consecutive numbering, for example slide01.nrrd, slide02,nrrd, slide03.nrrd, ...). Once you have verified that this approach works, you can write scripts to automate the process.

Andras


-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Andrey Fedorov
Sent: February 14, 2017 13:07
To: Jeff Ellis <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Saltz, Joel <[hidden email]>; Bremer, Erich <[hidden email]>
Subject: Re: [slicer-users] Visualization and Analysis of 3D Microscopic Images

I am not an expert in digital pathology, but I can give you some answers based on my understanding. I also cc the team behind SlicerPathology so they can provide more guidance hopefully.

>
> 1.  Any advice on how best to scan the slides initially?  Format to
> use?  Is there a nomenclature to use when saving the images so the
> software understands the order of the slides?  Do I simply save .jpg
> files and number them 1.jpg 2.jpg 3.jpg etc and upload the folder with all??
>

The format most likely be determined by the scanner and software.
Quite often those scanners use proprietary formats, which are not compatible with 3D Slicer, and you may need to use additional tools for conversion (such as OpenSlide http://openslide.org/). The resulting images may be too large to interact with using Slicer.

> 2. Any advice on how to "line up" one slide to the next?  Or does the
> program do this for us?  These (unlike an MRI scan) will be hand
> mounted on glass slices, and may need digital alignment from one slide to the next??
>

Slicer does not have custom tools to help with this task. You can load individual sections and use Slicer Transform module to align them, but you may be able to find more customized tools for this task. Someone mentioned to me TrakEM2 for this task:
http://www.ini.uzh.ch/~acardona/trakem2.html, but I have not tried it myself.

At this time, SlicerPathology can help you with segmenting cell nuclei in (relatively) small patches of digital pathology images. The input images should be in one of the non-proprietary formats that can be read by Slicer (such as gif, tiff, or jpg).

> 3. Any thoughts on the appropriate step thickness through the tissue block?
> How many slides to make? Or if there is a limit I should try to stay under?
>

I don't have relevant practical experience to give you advice on this one... I think for the most part this will be limited by the resources you have to process the volume of the thin sections you will be collecting.

> Any practical advice would be most helpful. I apologize if these are
> all very basic questions, but I could not find any documentation or
> sample slide sets to help be better understand how to best approach this.
>
> Looking forward to your thoughts.
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Fal


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Visualization and Analysis of 3D Microscopic Images

Jeff Ellis
In reply to this post by Andrey Fedorov-2
Thank you Andras and Thank you Andrey!
Both of your comments are very helpful.

For our specific project, we do not need to line tissue up with other imaging, so gold markers implanted prior to excision of tissue may not be helpful.  Though I don't have personal experience with this.... do these radiographic markers appear on the histology slides?  I'm surprised they wouldn't get washed off or cause a problem with the blade of the microtome?  Anyone with experience here?

I am focused on how to line up the histology sections.  Perhaps have markers been added to the paraffin wax block itself to help orient and align tissue in a semi-automated (or even manual) way?

http://www.ini.uzh.ch/~acardona/howto.html Looks to be an outstanding resource, and I'm excited to download and work with it.

Thank you also tIlya Belevich who has also made the suggestions, which I am looking into including Matlab and MIB (http://mib.helsinki.fi)
As well as the potnetnail for specialized microtomes for the task which exist for EM work (i.e.http://www.gatan.com/products/sem-imaging-spectroscopy/3view-system ) but do not seem to exist for light microscopy.  

Any further comments or ideas are very much appreciated.
Thank you again
Jeff



On Tue, Feb 14, 2017 at 11:18 PM, Andras Lasso <[hidden email]> wrote:

Unless you can set up imaging that provides perfectly aligned histology image slices, you’ll need retrospective alignment. There is probably no simpler way of aligning images than using landmarks. Of course you need to have clearly identifiable landmarks, so you may have to add those, if there are no good inherent landmarks in the images.

 

Visual alignment is quick and easy if you only have translation, but if you also have rotation and potentially slight deformations, then it takes a lot of iterations to find good alignment. Landmark registration is very simple and predictable and can easily handle translation, rotation, and even deformation.

 

Andras

 

From: Andrey Fedorov [mailto:[hidden email]]
Sent: February 14, 2017 23:06
To: Andras Lasso <[hidden email]>
Cc: [hidden email]; Bremer, Erich <[hidden email]>; Saltz, Joel <[hidden email]>; Jeff Ellis <[hidden email]>
Subject: RE: [slicer-users] Visualization and Analysis of 3D Microscopic Images

 

Andras, I believe the main purpose of the strands was to facilitate MRI to pathology registration. If MRI registration is not the objective, the process does not necessarily need to be that involved. (and even if it is - applicability of this approach for organs other than prostate remains to be demonstrated)

 

Don't get me wrong, Ward et al is a great approach for the specific task, and for someone with a lot of resources, but we should not overcomplicate the problem without necessity.

 

On Feb 14, 2017 18:19, "Andras Lasso" <[hidden email]> wrote:

Aaron Ward's group worked a lot on reconstructing 3D volume from histology images slices (and registering to MRI volumes). They tried many different methods to register slices to each other, but finally ended up using strand-shaped fiducials. See for example this paper:
http://onlinelibrary.wiley.com/doi/10.1002/jmri.23767/abstract

In Slicer you can use the Fiducial registration wizard module (in SlicerIGT extension) to register slides to each other based on marked fiducial positions. Once you have the alignment transform, you would need to use the Resample volume module to resample the aligned slice on a common grid, and save the slice to file. Once you've registered all the slides, you can load the sequence of images as a volume (you just have to assign file names that have consecutive numbering, for example slide01.nrrd, slide02,nrrd, slide03.nrrd, ...). Once you have verified that this approach works, you can write scripts to automate the process.

Andras


-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Andrey Fedorov
Sent: February 14, 2017 13:07
To: Jeff Ellis <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Saltz, Joel <[hidden email]>; Bremer, Erich <[hidden email]>
Subject: Re: [slicer-users] Visualization and Analysis of 3D Microscopic Images

I am not an expert in digital pathology, but I can give you some answers based on my understanding. I also cc the team behind SlicerPathology so they can provide more guidance hopefully.

>
> 1.  Any advice on how best to scan the slides initially?  Format to
> use?  Is there a nomenclature to use when saving the images so the
> software understands the order of the slides?  Do I simply save .jpg
> files and number them 1.jpg 2.jpg 3.jpg etc and upload the folder with all??
>

The format most likely be determined by the scanner and software.
Quite often those scanners use proprietary formats, which are not compatible with 3D Slicer, and you may need to use additional tools for conversion (such as OpenSlide http://openslide.org/). The resulting images may be too large to interact with using Slicer.

> 2. Any advice on how to "line up" one slide to the next?  Or does the
> program do this for us?  These (unlike an MRI scan) will be hand
> mounted on glass slices, and may need digital alignment from one slide to the next??
>

Slicer does not have custom tools to help with this task. You can load individual sections and use Slicer Transform module to align them, but you may be able to find more customized tools for this task. Someone mentioned to me TrakEM2 for this task:
http://www.ini.uzh.ch/~acardona/trakem2.html, but I have not tried it myself.

At this time, SlicerPathology can help you with segmenting cell nuclei in (relatively) small patches of digital pathology images. The input images should be in one of the non-proprietary formats that can be read by Slicer (such as gif, tiff, or jpg).

> 3. Any thoughts on the appropriate step thickness through the tissue block?
> How many slides to make? Or if there is a limit I should try to stay under?
>

I don't have relevant practical experience to give you advice on this one... I think for the most part this will be limited by the resources you have to process the volume of the thin sections you will be collecting.

> Any practical advice would be most helpful. I apologize if these are
> all very basic questions, but I could not find any documentation or
> sample slide sets to help be better understand how to best approach this.
>
> Looking forward to your thoughts.
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Fal



_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Visualization and Analysis of 3D Microscopic Images

Andras Lasso-2
In reply to this post by Andrey Fedorov-2

In the paper I referred to (“Registration of Prostate Histology Images to Ex Vivo MR Images Via Strand-Shaped Fiducials”, http://onlinelibrary.wiley.com/doi/10.1002/jmri.23767/epdf), they don’t use gold markers but strand-shaped fiducials, one made of cotton the other from animal tissue, infused in tissue marking dye.

 

Andras

 

From: Jeff Ellis [mailto:[hidden email]]
Sent: February 15, 2017 16:18
To: Andras Lasso <[hidden email]>
Cc: Andrey Fedorov <[hidden email]>; [hidden email]; Bremer, Erich <[hidden email]>; Saltz, Joel <[hidden email]>
Subject: Re: [slicer-users] Visualization and Analysis of 3D Microscopic Images

 

Thank you Andras and Thank you Andrey!

Both of your comments are very helpful.

 

For our specific project, we do not need to line tissue up with other imaging, so gold markers implanted prior to excision of tissue may not be helpful.  Though I don't have personal experience with this.... do these radiographic markers appear on the histology slides?  I'm surprised they wouldn't get washed off or cause a problem with the blade of the microtome?  Anyone with experience here?

 

I am focused on how to line up the histology sections.  Perhaps have markers been added to the paraffin wax block itself to help orient and align tissue in a semi-automated (or even manual) way?

 

http://www.ini.uzh.ch/~acardona/howto.html Looks to be an outstanding resource, and I'm excited to download and work with it.

 

Thank you also tIlya Belevich who has also made the suggestions, which I am looking into including Matlab and MIB (http://mib.helsinki.fi)

As well as the potnetnail for specialized microtomes for the task which exist for EM work (i.e.http://www.gatan.com/products/sem-imaging-spectroscopy/3view-system ) but do not seem to exist for light microscopy.  

 

Any further comments or ideas are very much appreciated.

Thank you again

Jeff

 

 

 

On Tue, Feb 14, 2017 at 11:18 PM, Andras Lasso <[hidden email]> wrote:

Unless you can set up imaging that provides perfectly aligned histology image slices, you’ll need retrospective alignment. There is probably no simpler way of aligning images than using landmarks. Of course you need to have clearly identifiable landmarks, so you may have to add those, if there are no good inherent landmarks in the images.

 

Visual alignment is quick and easy if you only have translation, but if you also have rotation and potentially slight deformations, then it takes a lot of iterations to find good alignment. Landmark registration is very simple and predictable and can easily handle translation, rotation, and even deformation.

 

Andras

 

From: Andrey Fedorov [mailto:[hidden email]]
Sent: February 14, 2017 23:06
To: Andras Lasso <[hidden email]>
Cc: [hidden email]; Bremer, Erich <[hidden email]>; Saltz, Joel <[hidden email]>; Jeff Ellis <[hidden email]>
Subject: RE: [slicer-users] Visualization and Analysis of 3D Microscopic Images

 

Andras, I believe the main purpose of the strands was to facilitate MRI to pathology registration. If MRI registration is not the objective, the process does not necessarily need to be that involved. (and even if it is - applicability of this approach for organs other than prostate remains to be demonstrated)

 

Don't get me wrong, Ward et al is a great approach for the specific task, and for someone with a lot of resources, but we should not overcomplicate the problem without necessity.

 

On Feb 14, 2017 18:19, "Andras Lasso" <[hidden email]> wrote:

Aaron Ward's group worked a lot on reconstructing 3D volume from histology images slices (and registering to MRI volumes). They tried many different methods to register slices to each other, but finally ended up using strand-shaped fiducials. See for example this paper:
http://onlinelibrary.wiley.com/doi/10.1002/jmri.23767/abstract

In Slicer you can use the Fiducial registration wizard module (in SlicerIGT extension) to register slides to each other based on marked fiducial positions. Once you have the alignment transform, you would need to use the Resample volume module to resample the aligned slice on a common grid, and save the slice to file. Once you've registered all the slides, you can load the sequence of images as a volume (you just have to assign file names that have consecutive numbering, for example slide01.nrrd, slide02,nrrd, slide03.nrrd, ...). Once you have verified that this approach works, you can write scripts to automate the process.

Andras


-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Andrey Fedorov
Sent: February 14, 2017 13:07
To: Jeff Ellis <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Saltz, Joel <[hidden email]>; Bremer, Erich <[hidden email]>
Subject: Re: [slicer-users] Visualization and Analysis of 3D Microscopic Images

I am not an expert in digital pathology, but I can give you some answers based on my understanding. I also cc the team behind SlicerPathology so they can provide more guidance hopefully.

>
> 1.  Any advice on how best to scan the slides initially?  Format to
> use?  Is there a nomenclature to use when saving the images so the
> software understands the order of the slides?  Do I simply save .jpg
> files and number them 1.jpg 2.jpg 3.jpg etc and upload the folder with all??
>

The format most likely be determined by the scanner and software.
Quite often those scanners use proprietary formats, which are not compatible with 3D Slicer, and you may need to use additional tools for conversion (such as OpenSlide http://openslide.org/). The resulting images may be too large to interact with using Slicer.

> 2. Any advice on how to "line up" one slide to the next?  Or does the
> program do this for us?  These (unlike an MRI scan) will be hand
> mounted on glass slices, and may need digital alignment from one slide to the next??
>

Slicer does not have custom tools to help with this task. You can load individual sections and use Slicer Transform module to align them, but you may be able to find more customized tools for this task. Someone mentioned to me TrakEM2 for this task:
http://www.ini.uzh.ch/~acardona/trakem2.html, but I have not tried it myself.

At this time, SlicerPathology can help you with segmenting cell nuclei in (relatively) small patches of digital pathology images. The input images should be in one of the non-proprietary formats that can be read by Slicer (such as gif, tiff, or jpg).

> 3. Any thoughts on the appropriate step thickness through the tissue block?
> How many slides to make? Or if there is a limit I should try to stay under?
>

I don't have relevant practical experience to give you advice on this one... I think for the most part this will be limited by the resources you have to process the volume of the thin sections you will be collecting.

> Any practical advice would be most helpful. I apologize if these are
> all very basic questions, but I could not find any documentation or
> sample slide sets to help be better understand how to best approach this.
>
> Looking forward to your thoughts.
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Fal

 


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Visualization and Analysis of 3D Microscopic Images

Jeff Ellis
In reply to this post by Andrey Fedorov-2
Thank you for that
On Wed, Feb 15, 2017 at 4:41 PM Andras Lasso <[hidden email]> wrote:

In the paper I referred to (“Registration of Prostate Histology Images to Ex Vivo MR Images Via Strand-Shaped Fiducials”, http://onlinelibrary.wiley.com/doi/10.1002/jmri.23767/epdf), they don’t use gold markers but strand-shaped fiducials, one made of cotton the other from animal tissue, infused in tissue marking dye.

 

Andras

 

From: Jeff Ellis [mailto:[hidden email]]
Sent: February 15, 2017 16:18
To: Andras Lasso <[hidden email]>
Cc: Andrey Fedorov <[hidden email]>; [hidden email]; Bremer, Erich <[hidden email]>; Saltz, Joel <[hidden email]>


Subject: Re: [slicer-users] Visualization and Analysis of 3D Microscopic Images

 

Thank you Andras and Thank you Andrey!

Both of your comments are very helpful.

 

For our specific project, we do not need to line tissue up with other imaging, so gold markers implanted prior to excision of tissue may not be helpful.  Though I don't have personal experience with this.... do these radiographic markers appear on the histology slides?  I'm surprised they wouldn't get washed off or cause a problem with the blade of the microtome?  Anyone with experience here?

 

I am focused on how to line up the histology sections.  Perhaps have markers been added to the paraffin wax block itself to help orient and align tissue in a semi-automated (or even manual) way?

 

http://www.ini.uzh.ch/~acardona/howto.html Looks to be an outstanding resource, and I'm excited to download and work with it.

 

Thank you also tIlya Belevich who has also made the suggestions, which I am looking into including Matlab and MIB (http://mib.helsinki.fi)

As well as the potnetnail for specialized microtomes for the task which exist for EM work (i.e.http://www.gatan.com/products/sem-imaging-spectroscopy/3view-system ) but do not seem to exist for light microscopy.  

 

Any further comments or ideas are very much appreciated.

Thank you again

Jeff

 

 

 

On Tue, Feb 14, 2017 at 11:18 PM, Andras Lasso <[hidden email]> wrote:

Unless you can set up imaging that provides perfectly aligned histology image slices, you’ll need retrospective alignment. There is probably no simpler way of aligning images than using landmarks. Of course you need to have clearly identifiable landmarks, so you may have to add those, if there are no good inherent landmarks in the images.

 

Visual alignment is quick and easy if you only have translation, but if you also have rotation and potentially slight deformations, then it takes a lot of iterations to find good alignment. Landmark registration is very simple and predictable and can easily handle translation, rotation, and even deformation.

 

Andras

 

From: Andrey Fedorov [mailto:[hidden email]]
Sent: February 14, 2017 23:06
To: Andras Lasso <[hidden email]>
Cc: [hidden email]; Bremer, Erich <[hidden email]>; Saltz, Joel <[hidden email]>; Jeff Ellis <[hidden email]>
Subject: RE: [slicer-users] Visualization and Analysis of 3D Microscopic Images

 

Andras, I believe the main purpose of the strands was to facilitate MRI to pathology registration. If MRI registration is not the objective, the process does not necessarily need to be that involved. (and even if it is - applicability of this approach for organs other than prostate remains to be demonstrated)

 

Don't get me wrong, Ward et al is a great approach for the specific task, and for someone with a lot of resources, but we should not overcomplicate the problem without necessity.

 

On Feb 14, 2017 18:19, "Andras Lasso" <[hidden email]> wrote:

Aaron Ward's group worked a lot on reconstructing 3D volume from histology images slices (and registering to MRI volumes). They tried many different methods to register slices to each other, but finally ended up using strand-shaped fiducials. See for example this paper:
http://onlinelibrary.wiley.com/doi/10.1002/jmri.23767/abstract

In Slicer you can use the Fiducial registration wizard module (in SlicerIGT extension) to register slides to each other based on marked fiducial positions. Once you have the alignment transform, you would need to use the Resample volume module to resample the aligned slice on a common grid, and save the slice to file. Once you've registered all the slides, you can load the sequence of images as a volume (you just have to assign file names that have consecutive numbering, for example slide01.nrrd, slide02,nrrd, slide03.nrrd, ...). Once you have verified that this approach works, you can write scripts to automate the process.

Andras


-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Andrey Fedorov
Sent: February 14, 2017 13:07
To: Jeff Ellis <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Saltz, Joel <[hidden email]>; Bremer, Erich <[hidden email]>
Subject: Re: [slicer-users] Visualization and Analysis of 3D Microscopic Images

I am not an expert in digital pathology, but I can give you some answers based on my understanding. I also cc the team behind SlicerPathology so they can provide more guidance hopefully.

>
> 1.  Any advice on how best to scan the slides initially?  Format to
> use?  Is there a nomenclature to use when saving the images so the
> software understands the order of the slides?  Do I simply save .jpg
> files and number them 1.jpg 2.jpg 3.jpg etc and upload the folder with all??
>

The format most likely be determined by the scanner and software.
Quite often those scanners use proprietary formats, which are not compatible with 3D Slicer, and you may need to use additional tools for conversion (such as OpenSlide http://openslide.org/). The resulting images may be too large to interact with using Slicer.

> 2. Any advice on how to "line up" one slide to the next?  Or does the
> program do this for us?  These (unlike an MRI scan) will be hand
> mounted on glass slices, and may need digital alignment from one slide to the next??
>

Slicer does not have custom tools to help with this task. You can load individual sections and use Slicer Transform module to align them, but you may be able to find more customized tools for this task. Someone mentioned to me TrakEM2 for this task:
http://www.ini.uzh.ch/~acardona/trakem2.html, but I have not tried it myself.

At this time, SlicerPathology can help you with segmenting cell nuclei in (relatively) small patches of digital pathology images. The input images should be in one of the non-proprietary formats that can be read by Slicer (such as gif, tiff, or jpg).

> 3. Any thoughts on the appropriate step thickness through the tissue block?
> How many slides to make? Or if there is a limit I should try to stay under?
>

I don't have relevant practical experience to give you advice on this one... I think for the most part this will be limited by the resources you have to process the volume of the thin sections you will be collecting.

> Any practical advice would be most helpful. I apologize if these are
> all very basic questions, but I could not find any documentation or
> sample slide sets to help be better understand how to best approach this.
>
> Looking forward to your thoughts.
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Fal

 


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Visualization and Analysis of 3D Microscopic Images

Fernando Pérez-García
You can also check Icy [1]


2017-02-15 22:46 GMT+01:00 Jeff Ellis <[hidden email]>:
Thank you for that
On Wed, Feb 15, 2017 at 4:41 PM Andras Lasso <[hidden email]> wrote:

In the paper I referred to (“Registration of Prostate Histology Images to Ex Vivo MR Images Via Strand-Shaped Fiducials”, http://onlinelibrary.wiley.com/doi/10.1002/jmri.23767/epdf), they don’t use gold markers but strand-shaped fiducials, one made of cotton the other from animal tissue, infused in tissue marking dye.

 

Andras

 

From: Jeff Ellis [mailto:[hidden email]]
Sent: February 15, 2017 16:18
To: Andras Lasso <[hidden email]>
Cc: Andrey Fedorov <[hidden email]>; [hidden email]; Bremer, Erich <[hidden email]>; Saltz, Joel <[hidden email]>


Subject: Re: [slicer-users] Visualization and Analysis of 3D Microscopic Images

 

Thank you Andras and Thank you Andrey!

Both of your comments are very helpful.

 

For our specific project, we do not need to line tissue up with other imaging, so gold markers implanted prior to excision of tissue may not be helpful.  Though I don't have personal experience with this.... do these radiographic markers appear on the histology slides?  I'm surprised they wouldn't get washed off or cause a problem with the blade of the microtome?  Anyone with experience here?

 

I am focused on how to line up the histology sections.  Perhaps have markers been added to the paraffin wax block itself to help orient and align tissue in a semi-automated (or even manual) way?

 

http://www.ini.uzh.ch/~acardona/howto.html Looks to be an outstanding resource, and I'm excited to download and work with it.

 

Thank you also tIlya Belevich who has also made the suggestions, which I am looking into including Matlab and MIB (http://mib.helsinki.fi)

As well as the potnetnail for specialized microtomes for the task which exist for EM work (i.e.http://www.gatan.com/products/sem-imaging-spectroscopy/3view-system ) but do not seem to exist for light microscopy.  

 

Any further comments or ideas are very much appreciated.

Thank you again

Jeff

 

 

 

On Tue, Feb 14, 2017 at 11:18 PM, Andras Lasso <[hidden email]> wrote:

Unless you can set up imaging that provides perfectly aligned histology image slices, you’ll need retrospective alignment. There is probably no simpler way of aligning images than using landmarks. Of course you need to have clearly identifiable landmarks, so you may have to add those, if there are no good inherent landmarks in the images.

 

Visual alignment is quick and easy if you only have translation, but if you also have rotation and potentially slight deformations, then it takes a lot of iterations to find good alignment. Landmark registration is very simple and predictable and can easily handle translation, rotation, and even deformation.

 

Andras

 

From: Andrey Fedorov [mailto:[hidden email]]
Sent: February 14, 2017 23:06
To: Andras Lasso <[hidden email]>
Cc: [hidden email]; Bremer, Erich <[hidden email]>; Saltz, Joel <[hidden email]>; Jeff Ellis <[hidden email]>
Subject: RE: [slicer-users] Visualization and Analysis of 3D Microscopic Images

 

Andras, I believe the main purpose of the strands was to facilitate MRI to pathology registration. If MRI registration is not the objective, the process does not necessarily need to be that involved. (and even if it is - applicability of this approach for organs other than prostate remains to be demonstrated)

 

Don't get me wrong, Ward et al is a great approach for the specific task, and for someone with a lot of resources, but we should not overcomplicate the problem without necessity.

 

On Feb 14, 2017 18:19, "Andras Lasso" <[hidden email]> wrote:

Aaron Ward's group worked a lot on reconstructing 3D volume from histology images slices (and registering to MRI volumes). They tried many different methods to register slices to each other, but finally ended up using strand-shaped fiducials. See for example this paper:
http://onlinelibrary.wiley.com/doi/10.1002/jmri.23767/abstract

In Slicer you can use the Fiducial registration wizard module (in SlicerIGT extension) to register slides to each other based on marked fiducial positions. Once you have the alignment transform, you would need to use the Resample volume module to resample the aligned slice on a common grid, and save the slice to file. Once you've registered all the slides, you can load the sequence of images as a volume (you just have to assign file names that have consecutive numbering, for example slide01.nrrd, slide02,nrrd, slide03.nrrd, ...). Once you have verified that this approach works, you can write scripts to automate the process.

Andras


-----Original Message-----
From: slicer-users [mailto:[hidden email]] On Behalf Of Andrey Fedorov
Sent: February 14, 2017 13:07
To: Jeff Ellis <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Saltz, Joel <[hidden email]>; Bremer, Erich <[hidden email]>
Subject: Re: [slicer-users] Visualization and Analysis of 3D Microscopic Images

I am not an expert in digital pathology, but I can give you some answers based on my understanding. I also cc the team behind SlicerPathology so they can provide more guidance hopefully.

>
> 1.  Any advice on how best to scan the slides initially?  Format to
> use?  Is there a nomenclature to use when saving the images so the
> software understands the order of the slides?  Do I simply save .jpg
> files and number them 1.jpg 2.jpg 3.jpg etc and upload the folder with all??
>

The format most likely be determined by the scanner and software.
Quite often those scanners use proprietary formats, which are not compatible with 3D Slicer, and you may need to use additional tools for conversion (such as OpenSlide http://openslide.org/). The resulting images may be too large to interact with using Slicer.

> 2. Any advice on how to "line up" one slide to the next?  Or does the
> program do this for us?  These (unlike an MRI scan) will be hand
> mounted on glass slices, and may need digital alignment from one slide to the next??
>

Slicer does not have custom tools to help with this task. You can load individual sections and use Slicer Transform module to align them, but you may be able to find more customized tools for this task. Someone mentioned to me TrakEM2 for this task:
http://www.ini.uzh.ch/~acardona/trakem2.html, but I have not tried it myself.

At this time, SlicerPathology can help you with segmenting cell nuclei in (relatively) small patches of digital pathology images. The input images should be in one of the non-proprietary formats that can be read by Slicer (such as gif, tiff, or jpg).

> 3. Any thoughts on the appropriate step thickness through the tissue block?
> How many slides to make? Or if there is a limit I should try to stay under?
>

I don't have relevant practical experience to give you advice on this one... I think for the most part this will be limited by the resources you have to process the volume of the thin sections you will be collecting.

> Any practical advice would be most helpful. I apologize if these are
> all very basic questions, but I could not find any documentation or
> sample slide sets to help be better understand how to best approach this.
>
> Looking forward to your thoughts.
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Fal

 


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Get volume of a model programatically

Kent Ogden
In reply to this post by Andrey Fedorov-2
Hi Slicer users,
 
Can someone give me an example of how to get the volume of a model in the python interpreter in Slicer?  I have a large number of files to process so this would be the easiest way, instead of manually loading them then looking at the models module.  I can open the models easily using
 
temp = slicer.util.LoadModel("model name.stl", true)
 
but I don't know how to access the volume (actually I assume that it will need to be calculated first) that would be shown in the models module.
 
Thanks . . .
 
Kent
 

 
 
 
Kent Ogden PhD
Associate Professor, Radiology
SUNY Upstate Medical University
750 E. Adams Street
Syracuse, NY  13210

email:  [hidden email]
voice:  (315) 464-5083
fax:       (315) 464-8789
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Get volume of a model programatically

Fernando Pérez-García
Hi Kent,

Maybe you can do:
modelNode = slicer.util.loadModel("modelname.stl", returnNode=True)[1]
polyData = modelNode.GetPolyData()

And then use vtkMassProperties to calculate your volume. I think that's also the way Slicer calculates it.


Fernando

2017-02-16 16:32 GMT+01:00 Kent Ogden <[hidden email]>:
Hi Slicer users,
 
Can someone give me an example of how to get the volume of a model in the python interpreter in Slicer?  I have a large number of files to process so this would be the easiest way, instead of manually loading them then looking at the models module.  I can open the models easily using
 
temp = slicer.util.LoadModel("model name.stl", true)
 
but I don't know how to access the volume (actually I assume that it will need to be calculated first) that would be shown in the models module.
 
Thanks . . .
 
Kent
 

 
 
 
Kent Ogden PhD
Associate Professor, Radiology
SUNY Upstate Medical University
750 E. Adams Street
Syracuse, NY  13210

email:  [hidden email]
voice:  <a href="tel:(315)%20464-5083" value="&#43;13154645083" target="_blank">(315) 464-5083
fax:       <a href="tel:(315)%20464-8789" value="&#43;13154648789" target="_blank">(315) 464-8789

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: Get volume of a model programatically

Kent Ogden
In reply to this post by Kent Ogden
Fernando,
 
That's right.  I expanded your code to get the volume.  Thanks....
 
 
modelNode = slicer.util.loadModel("modelname.stl", returnNode=True)[1]
polyData = modelNode.GetPolyData()
mass = vtk.vtkMassProperties
mass.SetInputData(polyData)
mass.GetVolume()
 
 
 
This works fine.  Credit to one of my Residents, Petro Kostandy, who had also figured this out.
 
Kent
 
 
 
 
 

 
And then use vtkMassProperties to calculate your volume. I think that's also the way Slicer calculates it.


Fernando

2017-02-16 16:32 GMT+01:00 Kent Ogden <[hidden email]>:
Hi Slicer users,
Can someone give me an example of how to get the volume of a model in the python interpreter in Slicer? I have a large number of files to process so this would be the easiest way, instead of manually loading them then looking at the models module. I can open the models easily using
temp = slicer.util.LoadModel("model name.stl", true)
but I don't know how to access the volume (actually I assume that it will need to be calculated first) that would be shown in the models module.
Thanks . . .
Kent

Kent Ogden PhD
Associate Professor, Radiology
SUNY Upstate Medical University
750 E. Adams Street
Syracuse, NY 13210

email: [hidden email]
voice: <a href="tel:(315)%20464-5083" target="_blank" value="&#43;13154645083">(315) 464-5083
fax: <a href="tel:(315)%20464-8789" target="_blank" value="&#43;13154648789">(315) 464-8789

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ