3D reconstruction

[Carlos Lizama]

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Other Question,

I have a problem with a 3D reconstruction and the requirements that the
computer need to do it.

I have a video is a time-lapse video with multiple  z-plane. But I was trying to
do the 3d reconstruction with imagej, bioimageX but its impossible because
the video large its about 1.3 GB.
My question is can you give me a recomendation of the pc requirements and
other software to do a 3D reconstruction?.
I was trying to do it with  volocity to but for some reason volocity can do it
with the separated channel but when Im doing the merging of channel the
software collapse completly.

thanks

[Zac Arrac Atelaz]

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Hello Carlos: You might try doing partial reconstructions, spliting your T stack in smaller files and once you have the time and Z rendering put them back together. Some troubles analizing has more to do with software than hardware. Best regards Gabriel OH
 > Date: Mon, 28 May 2012 14:55:35 -0500

> From: [hidden email]
> Subject: 3D reconstruction
> To: [hidden email]
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Other Question,
>
> I have a problem with a 3D reconstruction and the requirements that the
> computer need to do it.
>
> I have a video is a time-lapse video with multiple  z-plane. But I was trying to
> do the 3d reconstruction with imagej, bioimageX but its impossible because
> the video large its about 1.3 GB.
> My question is can you give me a recomendation of the pc requirements and
> other software to do a 3D reconstruction?.
> I was trying to do it with  volocity to but for some reason volocity can do it
> with the separated channel but when Im doing the merging of channel the
> software collapse completly.
>
> thanks

     

[Cameron Nowell]

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Hi Carlos,

What are the specs of the PC you are currently using? A 1.3GB file is
not that large really and should be able to open on a decently spec'd
machine.

My recommendations would be as follows

For 2D analysis - so that's image filtering, segmentation, counting,
measuring, 2d time series.
CPU - Intel Core i7. One of the mid range 4 core (8 virtual) ones will
be sufficiently powerful enough. Going up to more physical cores, faster
cores, or multiple physical CPUs (this includes going to Xeon
processors) will add more potential grunt, but will exponentially
increase the price of your system. The multiple cores of any multicore
system will only be used if the software is capable of using it. Not all
applications are or can be multithreaded. MetaMorph (version 7) for
example only uses one core, while its NX counterpart is multithreaded
(but very limited). ImageJ or Fiji can use multiple cores and you can
see vast improvements in processing time when it does (e.g. in the
Advanced Weka Segmentation plugin).
RAM - this is the key thing to all image processing. If you CPU is a bit
slow things just take longer, if you don't have enough RAM something's
cannot be done. Bare minimum I would recommend is 8GB for very basic
stuff. 16 GB for more advanced and as much as you can fit for anything
else. I have had some processing algorithms take up 15GB of RAM to
process a 1000x1000 pixel image.

For 3D analysis - the spec above plus a high end graphics card. This
doesn't need to be one of the uber expensive Nvidia Quadro or AMD FireGL
workstation cards. It just needs to be a fast gamer card with a lot of
RAM in it. I would recommend Nvidia as then you have access to the CUDA
GPGPU system as well (there are several software platforms that can use
this - Matlab has a toolbox for it). So something like a current gen
Nvidia 680 GTX or 690 GTX with 2 or 3 GB of ram will be more than
sufficient to run anything you throw at it (within reason). Be aware
that a high end graphics card is going to need a lot of power and
cooling. So make sure you get a power supply and system case that is up
to the task.


Cheers


Cam


Cameron J. Nowell
Microscopy Manager
Centre for Advanced Microscopy
Ludwig Institute for Cancer Research Melbourne - Parkville Branch
PO Box 2008
Royal Melbourne Hospital
Victoria, 3050
AUSTRALIA
Office: [phone]
Mobile: [phone]
Fax: [phone]
Facility Website
Linked In Profile



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]]
On Behalf Of Carlos Lizama
Sent: Tuesday, 29 May 2012 5:56 AM
To: [hidden email]
Subject: 3D reconstruction

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Other Question,

I have a problem with a 3D reconstruction and the requirements that the
computer need to do it.

I have a video is a time-lapse video with multiple  z-plane. But I was
trying to do the 3d reconstruction with imagej, bioimageX but its
impossible because the video large its about 1.3 GB.
My question is can you give me a recomendation of the pc requirements
and other software to do a 3D reconstruction?.
I was trying to do it with  volocity to but for some reason volocity can
do it with the separated channel but when Im doing the merging of
channel the software collapse completly.

thanks


This communication is intended only for the named recipient and may contain information that is confidential, legally privileged or subject to copyright; the Ludwig Institute for Cancer Research Ltd does not waive any rights if you have received this communication in error.
The views expressed in this communication are those of the sender and do not necessarily reflect the views of the Ludwig Institute for Cancer Research Ltd.

[Graham Wright]

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Hi Carlos,

The commercial 3D software packages have fairly strict (and fairly high)
requirements in terms of computer specs as Cameron has nicely covered,
particularly with the graphics card - some examples below:

Volocity:
http://cellularimaging.perkinelmer.com/support/technical_notes/detail.php?id=263
Imaris: http://www.bitplane.com/go/system-requirements
Amira: http://www.amira.com/documentation/system-requirements.html

Another free option to look at would be Vaa3D:
http://vaa3d.org/

Regards,
Graham

--
*Graham Wright, PhD*
Microscopy Unit Manager

Institute of Medical Biology
8A Biomedical Grove, #06-06 Immunos, Singapore 138648

E:   [hidden email]
W:  http://www.imb.a-star.edu.sg/imu/

On 29 May 2012 08:02, Cameron Nowell <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi Carlos,
>
> What are the specs of the PC you are currently using? A 1.3GB file is
> not that large really and should be able to open on a decently spec'd
> machine.
>
> My recommendations would be as follows
>
> For 2D analysis - so that's image filtering, segmentation, counting,
> measuring, 2d time series.
> CPU - Intel Core i7. One of the mid range 4 core (8 virtual) ones will
> be sufficiently powerful enough. Going up to more physical cores, faster
> cores, or multiple physical CPUs (this includes going to Xeon
> processors) will add more potential grunt, but will exponentially
> increase the price of your system. The multiple cores of any multicore
> system will only be used if the software is capable of using it. Not all
> applications are or can be multithreaded. MetaMorph (version 7) for
> example only uses one core, while its NX counterpart is multithreaded
> (but very limited). ImageJ or Fiji can use multiple cores and you can
> see vast improvements in processing time when it does (e.g. in the
> Advanced Weka Segmentation plugin).
> RAM - this is the key thing to all image processing. If you CPU is a bit
> slow things just take longer, if you don't have enough RAM something's
> cannot be done. Bare minimum I would recommend is 8GB for very basic
> stuff. 16 GB for more advanced and as much as you can fit for anything
> else. I have had some processing algorithms take up 15GB of RAM to
> process a 1000x1000 pixel image.
>
> For 3D analysis - the spec above plus a high end graphics card. This
> doesn't need to be one of the uber expensive Nvidia Quadro or AMD FireGL
> workstation cards. It just needs to be a fast gamer card with a lot of
> RAM in it. I would recommend Nvidia as then you have access to the CUDA
> GPGPU system as well (there are several software platforms that can use
> this - Matlab has a toolbox for it). So something like a current gen
> Nvidia 680 GTX or 690 GTX with 2 or 3 GB of ram will be more than
> sufficient to run anything you throw at it (within reason). Be aware
> that a high end graphics card is going to need a lot of power and
> cooling. So make sure you get a power supply and system case that is up
> to the task.
>
>
> Cheers
>
>
> Cam
>
>
> Cameron J. Nowell
> Microscopy Manager
> Centre for Advanced Microscopy
> Ludwig Institute for Cancer Research Melbourne - Parkville Branch
> PO Box 2008
> Royal Melbourne Hospital
> Victoria, 3050
> AUSTRALIA
> Office: [phone]
> Mobile: [phone]
> Fax: [phone]
> Facility Website
> Linked In Profile
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Carlos Lizama
> Sent: Tuesday, 29 May 2012 5:56 AM
> To: [hidden email]
> Subject: 3D reconstruction
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Other Question,
>
> I have a problem with a 3D reconstruction and the requirements that the
> computer need to do it.
>
> I have a video is a time-lapse video with multiple  z-plane. But I was
> trying to do the 3d reconstruction with imagej, bioimageX but its
> impossible because the video large its about 1.3 GB.
> My question is can you give me a recomendation of the pc requirements
> and other software to do a 3D reconstruction?.
> I was trying to do it with  volocity to but for some reason volocity can
> do it with the separated channel but when Im doing the merging of
> channel the software collapse completly.
>
> thanks
>
>
> This communication is intended only for the named recipient and may
> contain information that is confidential, legally privileged or subject to
> copyright; the Ludwig Institute for Cancer Research Ltd does not waive any
> rights if you have received this communication in error.
> The views expressed in this communication are those of the sender and do
> not necessarily reflect the views of the Ludwig Institute for Cancer
> Research Ltd.
>

[Steffen Dietzel]

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To join, leave or search the confocal microscopy listserv, go to:
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Carlos,

what system are you using now? You probably can do this with ImageJ, but
only with the 64 bit version. The 32 bit version can handle only about
1.4 RAM for Java so that you should be able to open your file but you
cannot manipulate it ("out of memmory").

So you should use e.g. Win7-64 bit or a 64 bit Linux on a machine with
at least 4 GB of RAM. If you go shopping anyway take more, Cam gave you
some good hardware suggestions.

Personally, I like Bitplane Imaris for the things you have described.
Not exactly a bargain, though. But I am sure your local representative
will provide you with a free 30-day test version. As for other software,
you can find the hardware requirements on their web site.

Steffen

On 28.05.2012 21:55, Carlos Lizama wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Other Question,
>
> I have a problem with a 3D reconstruction and the requirements that the
> computer need to do it.
>
> I have a video is a time-lapse video with multiple  z-plane. But I was trying to
> do the 3d reconstruction with imagej, bioimageX but its impossible because
> the video large its about 1.3 GB.
> My question is can you give me a recomendation of the pc requirements and
> other software to do a 3D reconstruction?.
> I was trying to do it with  volocity to but for some reason volocity can do it
> with the separated channel but when Im doing the merging of channel the
> software collapse completly.
>
> thanks
>

--
------------------------------------------------------------
Steffen Dietzel, PD Dr. rer. nat
Ludwig-Maximilians-Universität München
Walter-Brendel-Zentrum für experimentelle Medizin (WBex)
Head of light microscopy

Mail room:
Marchioninistr. 15, D-81377 München

Building location:
Marchioninistr. 27,  München-Großhadern

[Vincent Schoonderwoert]

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/**commercial interest**/


Dear Carlos,

As a commercial company, we have to jump into this discussion because of
the statement regarding the need for advanced graphical cards for 3D
visualization.

Our software Huygens renders continuous surfaces with fast ray tracing
algorithms, so there is no need for any special graphic card as would be
necessary for conventional polygon based techniques. The fast ray
tracers can utilize 64 bit multiprocessor systems, and are therefore
able to render very large microscopic volume data to high resolution
output images.

If you render an image of 1.5 Gb with one of the three available Huygens
visualization options, no more than 3.5Gb of memory is consumed. We
tested a 1.5 Gb image on an inexpensive dual core (AMD Athlon(tm) II X2
270 Processor × 2) computer with 4Gb RAM and a simple graphical card.
This worked fine. However. I would advised to go for more RAM, because
it is not that expensive and would speed up the rendering process
significantly.
The 8Gb RAM that Cameron advised should be enough for the image size you
suggested.
If you are interested in testing Huygens just request a trial version
via our homepage at svi.nl

Best regards,
Vincent


***********************************************************
Vincent Schoonderwoert, PhD
Senior Imaging Specialist/Account Manager
Scientific Volume Imaging bv
Tel: + 31 35 646 8216
***********************************************************








On 05/28/2012 09:55 PM, Carlos Lizama wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Other Question,
>
> I have a problem with a 3D reconstruction and the requirements that the
> computer need to do it.
>
> I have a video is a time-lapse video with multiple  z-plane. But I was trying to
> do the 3d reconstruction with imagej, bioimageX but its impossible because
> the video large its about 1.3 GB.
> My question is can you give me a recomendation of the pc requirements and
> other software to do a 3D reconstruction?.
> I was trying to do it with  volocity to but for some reason volocity can do it
> with the separated channel but when Im doing the merging of channel the
> software collapse completly.
>
> thanks
>

[Carlos Lizama]

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http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Im using win7-64 bits and im using imageJ I change the memory option but i
think for my computer its too much. because the file size its about 1.4 gb,
has a z-stack each five minutes in time-lapse. Im going a try to do that in
other computer more powerfull. I m going to check the imaris option. Thanks
stefan.

On Tue, May 29, 2012 at 6:18 AM, Steffen Dietzel <[hidden email]>wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
> *****
>
> Carlos,
>
> what system are you using now? You probably can do this with ImageJ, but
> only with the 64 bit version. The 32 bit version can handle only about 1.4
> RAM for Java so that you should be able to open your file but you cannot
> manipulate it ("out of memmory").
>
> So you should use e.g. Win7-64 bit or a 64 bit Linux on a machine with at
> least 4 GB of RAM. If you go shopping anyway take more, Cam gave you some
> good hardware suggestions.
>
> Personally, I like Bitplane Imaris for the things you have described. Not
> exactly a bargain, though. But I am sure your local representative will
> provide you with a free 30-day test version. As for other software, you can
> find the hardware requirements on their web site.
>
> Steffen
>
>
> On 28.05.2012 21:55, Carlos Lizama wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
>> *****
>>
>> Other Question,
>>
>> I have a problem with a 3D reconstruction and the requirements that the
>> computer need to do it.
>>
>> I have a video is a time-lapse video with multiple  z-plane. But I was
>> trying to
>> do the 3d reconstruction with imagej, bioimageX but its impossible because
>> the video large its about 1.3 GB.
>> My question is can you give me a recomendation of the pc requirements and
>> other software to do a 3D reconstruction?.
>> I was trying to do it with  volocity to but for some reason volocity can
>> do it
>> with the separated channel but when Im doing the merging of channel the
>> software collapse completly.
>>
>> thanks
>>
>>
>
> --
> ------------------------------**------------------------------
> Steffen Dietzel, PD Dr. rer. nat
> Ludwig-Maximilians-Universität München
> Walter-Brendel-Zentrum für experimentelle Medizin (WBex)
> Head of light microscopy
>
> Mail room:
> Marchioninistr. 15, D-81377 München
>
> Building location:
> Marchioninistr. 27,  München-Großhadern
>

[John Hyun-2]

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To All:

I would like to invite you to a webinar reviewing the utility of Serial Block Face Scanning Electron Microscopy techniques to acquire large 3D volumes of electron microscope data. Please see webinar information below and a quick link to register for this event. Please contact me if you have any questions. Good luck with your research.

--
Best regards,

John Hyun
Marketing Communications Manager

Gatan, Inc.
Corporate Headquarters
5794 W.  Las Positas Blvd.
Pleasanton, CA 94588 USA

Tel:  [phone]
Fax: [phone]
Email: [hidden email]
Website:  www.gatan.com


Webinar: Acquire and quantify volumetric datasets, well beyond optical resolution with 3View, an automated 3D-EM imaging system
1:00-2:00 pm, US/Eastern (10:00-11:00 am, US/Pacific), Thursday, June 14, 2012

Complement Confocal Microcopy: Learn how to acquire large 3D volumes of electron microscope data, generate metrics and apply statistical analysis to 3D-EM data, with the speed of optical imaging and at resolutions rivaling the most expensive and complex transmission electron microscope (TEM) solutions.

Presenters:

  *   Dr. Grahame Kidd, Department of Neurosciences, Cleveland Clinic and Scientific Advisor to Renovo Neural, will discuss how Serial Block Face Scanning Electron Microscopy (SBFSEM) makes possible new, powerful quantitative assays that take advantage of EM resolution and three dimensionality to provide new insights into remyelination, mitochondrial structure, synapse organization and endoplasmic reticulum structure.
  *   Joel Mancuso, 3View Applications Manager, Gatan Inc., will elaborate on the mechanics of the SBFSEM technique and explain how it was developed to eliminate the traditional barriers to entry for collecting 3D-EM data with a simple and highly productive workflow.

REGISTRATION: To register for this special event, please log onto: http://www.gatan.com/products/3View_webinar.php. You will receive email confirmation of your registration followed by complete details and instructions to log into the live webinar. Space is limited. Please register by June 7, 2012. If you have any questions, please contact: [hidden email]. For more information on 3View, please log onto: http://www.gatan.com/products/sem_products/products/3View_landing.php. To view/download application and technical references, please log onto: http://www.gatan.com/products/sem_products/products/3View_Appnotes.php.

[Christian Götze]

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Commercial response!

Hi Carlos,

our software "arivis Vision 4D" is specialized in fast and easy handling
and visualization of large image stacks. A dataset of 1.5GByte should be
no problem to import, render and creating a movie out of it. Have a look
on a short demo at
http://www.youtube.com/watch?v=4Rwq3wgvTc0

You can download a free trial of "arivis Vision 4D" at
http://www.arivis.com/en/arivis-Vision-4D/Features

If there are any questions, please don't hesitate to contact me.

Best,
Christian

Am 28.05.2012 21:55, schrieb Carlos Lizama:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Other Question,
>
> I have a problem with a 3D reconstruction and the requirements that the
> computer need to do it.
>
> I have a video is a time-lapse video with multiple  z-plane. But I was trying to
> do the 3d reconstruction with imagej, bioimageX but its impossible because
> the video large its about 1.3 GB.
> My question is can you give me a recomendation of the pc requirements and
> other software to do a 3D reconstruction?.
> I was trying to do it with  volocity to but for some reason volocity can do it
> with the separated channel but when Im doing the merging of channel the
> software collapse completly.
>
> thanks

--
Christian Götze

arivis GmbH
Kröpeliner Straße 54, 18055 Rostock, Germany

Tel : [phone]
Fax : [phone]
Mail: [hidden email]
Web : http://www.arivis.com

Amtsgericht Rostock HRB 11940
Geschäftsführung: Andreas Suchanek, Christian Götze, Offer Dattner

[John Hyun-2]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

To All:

I would like to invite you to a webinar reviewing the utility of Serial Block Face Scanning Electron Microscopy techniques to acquire large 3D volumes of electron microscope data. Please see webinar information below and a quick link to register for this event. Please contact me if you have any questions. Good luck with your research.

--
Best regards,

John Hyun
Marketing Communications Manager

Gatan, Inc.
Corporate Headquarters
5794 W.  Las Positas Blvd.
Pleasanton, CA 94588 USA

Tel:  [phone]
Fax: [phone]
Email: [hidden email]<mailto:[hidden email]>
Website:  www.gatan.com


Webinar: Acquire and quantify volumetric datasets, well beyond optical resolution with 3View, an automated 3D-EM imaging system
1:00-2:00 pm, US/Eastern (10:00-11:00 am, US/Pacific), Thursday, June 14, 2012

Complement Confocal Microcopy: Learn how to acquire large 3D volumes of electron microscope data, generate metrics and apply statistical analysis to 3D-EM data, with the speed of optical imaging and at resolutions rivaling the most expensive and complex transmission electron microscope (TEM) solutions.

Presenters:

  *   Dr. Grahame Kidd, Department of Neurosciences, Cleveland Clinic and Scientific Advisor to Renovo Neural, will discuss how Serial Block Face Scanning Electron Microscopy (SBFSEM) makes possible new, powerful quantitative assays that take advantage of EM resolution and three dimensionality to provide new insights into remyelination, mitochondrial structure, synapse organization and endoplasmic reticulum structure.
  *   Joel Mancuso, 3View Applications Manager, Gatan Inc., will elaborate on the mechanics of the SBFSEM technique and explain how it was developed to eliminate the traditional barriers to entry for collecting 3D-EM data with a simple and highly productive workflow.

REGISTRATION: To register for this special event, please log onto: http://www.gatan.com/products/3View_webinar.php. You will receive email confirmation of your registration followed by complete details and instructions to log into the live webinar. Space is limited. Please register by June 7, 2012. If you have any questions, please contact: [hidden email]<mailto:[hidden email]>. For more information on 3View, please log onto: http://www.gatan.com/products/sem_products/products/3View_landing.php. To view/download application and technical references, please log onto: http://www.gatan.com/products/sem_products/products/3View_Appnotes.php.