Segmentation in 3D

[Eric Scarfone]

Hi List,

A recent post made me think to ask, here:
I need to segment small features in 3D stacks that can only be outlined manually.  Problem is that given their size, these structures are somwhat undersampled and the tool that I am using now does not permit to modify interpolation levels. The 3D objects that I get are too much smoothed out.

Anybody knows of a manual 3D segmentation tool that would help (without going via photoshop!)?

Eric

Eric Scarfone, PhD, CNRS,
Center for Hearing and communication Research
Department of Clinical Neuroscience
Karolinska Institutet

Postal Address:
CFH, M1:02
Karolinska Hospital,
SE-171 76 Stockholm, Sweden

Work: [phone],
Cell: [phone]
Fax: [phone]

email: [hidden email]
http://www.ki.se/cfh/

[Cameron Nowell]

Hi Eric,
 
I have had sucess getting it done in metamorph by segmenting individual slices and then making them into a stack that can then be analysed in any 3D software such as metamorph or imaris.
 
What is it about your small features that make them difficult to segment?
 
 
Cheers
 
Cam
 
 
 
Cameron J. Nowell
Microscpy Manager
Central Resource for Advanced Microscopy
Ludwig Insttue for Cancer Research
PO Box 2008
Royal Melbourne Hospital
Victoria, 3050
AUSTRALIA
 
Office: [phone]
Mobile: [phone]
Fax: [phone]
 
http://www.ludwig.edu.au/branch/research/platform/microscopy.htm
 

________________________________

From: Confocal Microscopy List on behalf of Eric Scarfone
Sent: Tue 1/09/2009 5:45 PM
To: [hidden email]
Subject: Segmentation in 3D



Hi List,

A recent post made me think to ask, here:
I need to segment small features in 3D stacks that can only be outlined manually.  Problem is that given their size, these structures are somwhat undersampled and the tool that I am using now does not permit to modify interpolation levels. The 3D objects that I get are too much smoothed out.

Anybody knows of a manual 3D segmentation tool that would help (without going via photoshop!)?

Eric

Eric Scarfone, PhD, CNRS,
Center for Hearing and communication Research
Department of Clinical Neuroscience
Karolinska Institutet

Postal Address:
CFH, M1:02
Karolinska Hospital,
SE-171 76 Stockholm, Sweden

Work: [phone],
Cell: [phone]
Fax: [phone]

email: [hidden email]
http://www.ki.se/cfh/ 

[Carol Bayles]

>
>Dear Colleague:
>
>Please join us at the fourth annual Northeast Regional Life Sciences
>Core Directors (NERLSCD) meeting that will be held November 9-11,
>2009, at Cornell University in Ithaca, NY.
>
>The NERLSCD 2009 meeting will be a regional forum for core facility
>directors and managers to network with colleagues, to learn about
>biotechnology advances and applications, and to discuss the
>challenges and results of implementing shared research resources.
>There will be presentations and discussion forums on operational
>issues facing biotechnology core laboratories.  There will be
>scientific sessions and technical workshops on genomics, proteomics,
>imaging, and other technologies, including next generation
>sequencing, microarrays, proteomics, metabolomics, optical imaging,
>flow cytometry, stem cells, nanobiotechnology, and bioinformatics.
>A core facility poster session will offer an opportunity for
>learning about regional life sciences shared resources and services.
>Participants will be able to post and to learn of core facility
>related employment opportunities.  A satellite meeting before the
>main conference will focus on laboratory robotics.
>Tours will be given of core facilities.  There will be an opening
>reception and numerous opportunities to network with colleagues.
>
>Registration and more information about the meeting can be found at
>http://www.nerlscd.org.  Registration will be limited, so please
>register early.
>
>We look forward to seeing you at the NERLSCD 2009 meeting!
>
>
>The NERLSCD 2009 Meeting Organizing Committee, including George
>Grills (Cornell University), Theodore Thannhauser (USDA-ARS),
>Timothy Hunter (University of Vermont), Pamela Scott Adams (Trudeau
>Institute), Stephen Bobin (Dartmouth Medical School), Michelle
>Detwiler (Roswell Park Cancer Institute), Katia Sol-Church (Center
>for Pediatric Research, NCC-Delaware), and Susanna Perkins
>(University of Massachusetts Medical School).

--
<><><><><><><><><><><><><><><><><><><><><>
Carol Bayles, Manager
Microscopy & Imaging Facility (MIF)
Life Sciences Core Lab Center
B46 Weill Hall
607-254-4860
607-254-6379 fax
http://cores.lifesciences.cornell.edu

Confocal and Multiphoton Microscopy
Nanobiotechnology Center
www.nbtc.cornell.edu

Cornell University
Ithaca NY 14853

[Mark Cannell]

Since no-one else has answered I'll try. Interpolated points are not
real and are fabricated data. This is only justifiable if the
interpolated values follow a smooth curve (surface) that passes through
the actual data points and assumes that the original data set was
sampled _correctly_. If the original data was not sampled correctly
(undersampled) you can get aliasing which introduces artifacts (high
spatial frequency components now appear in the low frequency domain).
Interpolation may also follow smoothed data when the spatial content is
reduced. There is no way you can (or should) increase spatial content
above that defined by Nyquist which was set by your initial data
acqusition.

This is why on the Vancouver course we stress the importance of
correctly sampling the data.

Cheers Mark

Eric Scarfone wrote:

>
> Hi List,
>
> A recent post made me think to ask, here:
> I need to segment small features in 3D stacks that can only be
> outlined manually.  Problem is that given their size, these structures
> are somwhat undersampled and the tool that I am using now does not
> permit to modify interpolation levels. The 3D objects that I get are
> too much smoothed out.
>
> Anybody knows of a manual 3D segmentation tool that would help
> (without going via photoshop!)?
>
> Eric
>
> Eric Scarfone, PhD, CNRS,
> Center for Hearing and communication Research
> Department of Clinical Neuroscience
> Karolinska Institutet
>
> Postal Address:
> CFH, M1:02
> Karolinska Hospital,
> SE-171 76 Stockholm, Sweden
>
> Work: [phone],
> Cell: [phone]
> Fax: [phone]
>
> email: [hidden email]
> http://www.ki.se/cfh/
>
>

[Eric Scarfone]

Hi Mark, Cameron,

I fully agree with Mark on the importance of sampling at the proper rate! However a question still bugs me on that one, should one follow the lead of objective resolution of should one be more concerned by the size of the object one wants to image.
I often find that using the objectiv'es NA to set pixel size imposes a zoom factor that cuts out large areas of the sample that I would wish to include in the frame...ando often going to lower mag invoves poorer light trasmission etc....

The present case however is somewhat of a counter example, since the objects I am trying to segment are details of large images. Would I still have access to the preparation/microcscope, I would definitely zoom in on those details. But I did not see them then and only have the image stacks to work with!

Thanks fo rthe suggetion to go via metamorph. I did use Photoshop that helps similarly!! But it is a detour ?;^)

Cheers

Eric

Eric Scarfone, PhD, CNRS,
Center for Hearing and communication Research
Department of Clinical Neuroscience
Karolinska Institutet

Postal Address:
CFH, M1:02
Karolinska Hospital,
SE-171 76 Stockholm, Sweden

Work: [phone],
Cell: [phone]
Fax: [phone]

email: [hidden email]
http://www.ki.se/cfh/


----- Original Message -----
From: Cameron Nowell <[hidden email]>
Date: Wednesday, September 2, 2009 6:30 am
Subject: Re: Segmentation in 3D
To: [hidden email]

> Hi Eric,
>
> I have had sucess getting it done in metamorph by segmenting
> individual slices and then making them into a stack that can then
> be analysed in any 3D software such as metamorph or imaris.
>
> What is it about your small features that make them difficult to
> segment?
>
> Cheers

>
> Cam
>
>
>
> Cameron J. Nowell
> Microscpy Manager
> Central Resource for Advanced Microscopy
> Ludwig Insttue for Cancer Research
> PO Box 2008
> Royal Melbourne Hospital
> Victoria, 3050
> AUSTRALIA
>
> Office: [phone]
> Mobile: [phone]
> Fax: [phone]
>
> http://www.ludwig.edu.au/branch/research/platform/microscopy.htm
>
>
> ________________________________
>
> From: Confocal Microscopy List on behalf of Eric Scarfone
> Sent: Tue 1/09/2009 5:45 PM
> To: [hidden email]
> Subject: Segmentation in 3D
>
>
>
> Hi List,
>
> A recent post made me think to ask, here:
> I need to segment small features in 3D stacks that can only be

> outlined manually. Problem is that given their size, these

> structures are somwhat undersampled and the tool that I am using
> now does not permit to modify interpolation levels. The 3D objects
> that I get are too much smoothed out.
>
> Anybody knows of a manual 3D segmentation tool that would help
> (without going via photoshop!)?
>
> Eric
>
> Eric Scarfone, PhD, CNRS,
> Center for Hearing and communication Research
> Department of Clinical Neuroscience
> Karolinska Institutet
>
> Postal Address:
> CFH, M1:02
> Karolinska Hospital,
> SE-171 76 Stockholm, Sweden
>
> Work: [phone],
> Cell: [phone]
> Fax: [phone]
>
> email: [hidden email]
> http://www.ki.se/cfh/
>

[Cesare -ALEMBIC-]

Dear All,
thinking to perform membrane repair assay in witch membrane damage is induced with a two-photon confocal laser-scanning (usually), I have a question:
Does it is possible perform this assay with a normal single photon confocal microscope as well?
Anybody has experienced it?

thank you very much!

Cesare



Dr. Cesare Covino
ALEMBIC
Advanced Light and Electron Microscopy BioImaging Center
San Raffaele Scientific Institute
via Olgettina 58, 20132 - Milano - Italy

----------------------------------------------------------------- La tua mano puo' lasciare un segno importante. Dona il tuo 5 per mille al San Raffaele di Milano. E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi "Finanziamento della ricerca sanitaria" il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Per saperne di piu': [hidden email] o vai sul sito http://www.5xmille.org.