Re: MetaMorph Journal to image wandering cells

[Houchaima Ben Tekaya]

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Hi all,

I am looking for a MetaMorph journal that would allow following migrating cells during acquisition of a time-lapse. Could somebody help?
Any other solution than a journal is also welcome.

Sincerely,
Houchaima

> Houchaima Ben-Tekaya
> Eng. Ph.D.
> Group of Prof. C. Dehio
> Division of Microbiology
> Biozentrum, University of Basel
> Klingelbergstrasse 50/70
> 4056 Basel
> Switzerland

[Romin, Yevgeniy/Sloan Kettering Institute]

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Hi Houchaima

Writing a journal that segments out a cell and then follows it in Metamorph can be tricky.  What you may want to try is writing a journal that will acquire a tiled scan image every timepoint.  The number of tiles will be dependent on how far your cells will be going and how long you image.  That is something I would try first.

Hope this helps,

Yevgeniy
________________________________________
From: Confocal Microscopy List [[hidden email]] On Behalf Of Houchaima Ben Tekaya [[hidden email]]
Sent: Monday, February 11, 2013 11:10 AM
To: [hidden email]
Subject: Re: MetaMorph Journal to image wandering cells

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Hi all,

I am looking for a MetaMorph journal that would allow following migrating cells during acquisition of a time-lapse. Could somebody help?
Any other solution than a journal is also welcome.

Sincerely,
Houchaima

> Houchaima Ben-Tekaya
> Eng. Ph.D.
> Group of Prof. C. Dehio
> Division of Microbiology
> Biozentrum, University of Basel
> Klingelbergstrasse 50/70
> 4056 Basel
> Switzerland


 
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[Cameron Nowell-2]

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Hi Houchaima,

As Yevgeniy has mentioned it can be tricky and will depend on the version of metamorph you have installed on the capture machine. That being said it is not impossible.

Will you have a single cell in the field or will it be a field full of cells. As suggested the other option would be to tile scan a larger area each time point.

Either of these things can be done. I already have some journals that do this, so I am happy to send you a copy to have a look at and get ideas from.

Just drop me a message off list with what you are going to be doing and I will sort something out.

Cheers

Cam



Cameron J. Nowell
Centre for Dynamic Imaging
The Walter and Eliza Hall Institute of Medical Research
1G Royal Parade
Parkville, Victoria 3052
Australia

Phone: [phone]
Mobile: [phone]
Fax: [phone]

Facility Website
LinkedIn Profile



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Houchaima Ben Tekaya
Sent: Tuesday, 12 February 2013 3:11 AM
To: [hidden email]
Subject: Re: MetaMorph Journal to image wandering cells

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Hi all,

I am looking for a MetaMorph journal that would allow following migrating cells during acquisition of a time-lapse. Could somebody help?
Any other solution than a journal is also welcome.

Sincerely,
Houchaima

> Houchaima Ben-Tekaya
> Eng. Ph.D.
> Group of Prof. C. Dehio
> Division of Microbiology
> Biozentrum, University of Basel
> Klingelbergstrasse 50/70
> 4056 Basel
> Switzerland

______________________________________________________________________
The information in this email is confidential and intended solely for the addressee.
You must not disclose, forward, print or use it without the permission of the sender.
______________________________________________________________________

[George McNamara]

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I prefer to separate acquisition from analysis. I recommend stage tiling
for acquisition (I hope you have a good stage and imaging mode that
stitching works well!). Then can use one of the motion apps (or
Integrated Morphometry Analysis/Measure Objects - either can be
journalized) for analysis.

On 2/11/2013 11:10 AM, Houchaima Ben Tekaya wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi all,
>
> I am looking for a MetaMorph journal that would allow following migrating cells during acquisition of a time-lapse. Could somebody help?
> Any other solution than a journal is also welcome.
>
> Sincerely,
> Houchaima
>
>    
>> Houchaima Ben-Tekaya
>> Eng. Ph.D.
>> Group of Prof. C. Dehio
>> Division of Microbiology
>> Biozentrum, University of Basel
>> Klingelbergstrasse 50/70
>> 4056 Basel
>> Switzerland
>>      
>    

[samuel connell]

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Commercial Response:

Hi Houchaima,

SlideBook software from 3i has the capabilities you are looking for. I
recognize you are likely already using your chosen software tools for your
application, but this simple response is also to inform the Confocal
Microscopy community of this additional commercial option.

Best Regards,

--
Sam Connell
Senior Applications Scientist
Intelligent Imaging Innovations
[hidden email]



On Wed, Feb 13, 2013 at 7:53 PM, George McNamara
<[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>
> *****
>
> I prefer to separate acquisition from analysis. I recommend stage tiling
> for acquisition (I hope you have a good stage and imaging mode that
> stitching works well!). Then can use one of the motion apps (or Integrated
> Morphometry Analysis/Measure Objects - either can be journalized) for
> analysis.
>
>
> On 2/11/2013 11:10 AM, Houchaima Ben Tekaya 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>
>> *****
>>
>> Hi all,
>>
>> I am looking for a MetaMorph journal that would allow following migrating
>> cells during acquisition of a time-lapse. Could somebody help?
>> Any other solution than a journal is also welcome.
>>
>> Sincerely,
>> Houchaima
>>
>>
>>
>>> Houchaima Ben-Tekaya
>>> Eng. Ph.D.
>>> Group of Prof. C. Dehio
>>> Division of Microbiology
>>> Biozentrum, University of Basel
>>> Klingelbergstrasse 50/70
>>> 4056 Basel
>>> Switzerland
>>>
>>>
>>
>>
>

[Vitaly Boyko]

We are having issues with accurate z positioning during xyz
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Dear All,

We are having issues with accurate z positioning during xyz scans on Zeiss Axiovert 200 under Metamorph in 'Asynchronous' mode (with total z in the range of 200 um, there are no issues within 70um). 
It is accurate under 'Synchronous' mode but xyz acquisition unacceptably slow.

These problems are seen only under 64-bit Windows (32-bit driver is OK).

Does anyone have similar issues and/or solution to the z drive accuracy?

Is anyone around who is responsible for bridging Zeiss and Molecular Devices? 

Is there anyone at MolDev who could "speak German"? 

Regards,

Vitaly
646-888-2186

[Arvydas Matiukas]

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Dear list,
 
Please share/advice what 3D printers you use to manufacture
parts for microscopy projects. BTW, what is good enough
material to make mechanical/microscopy parts from?
 
We are expanding our Confocal Microscopy Core along with
other Cores as we will be moving into a new research building,
and I would like to start using 3D printer. So far on the listserv
I found only mentioning of manufacturing some "crude boxes"
http://derisilab.ucsf.edu/index.php?page=3D
 
I found quite informative website
http://www.3dprinter.net/directory/personal-3d-printers
that lists many current manufacturers along with specs
and even awards. It would be very useful to know how
efficient/useful are these machines for microscopy projects.
 
Thanks,
Arvydas
----------------------------
 
 
 
Arvydas Matiukas, Ph.D.
Director of Confocal&Two-Photon Core
Department of Pharmacology
SUNY Upstate Medical University
766 Irving Ave., WH 3167
Syracuse, NY 13210
tel.: [phone]
fax: [phone]
email: [hidden email]

[Kurt Thorn]

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On 2/18/2013 8:08 AM, Arvydas Matiukas wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear list,
>  
> Please share/advice what 3D printers you use to manufacture
> parts for microscopy projects. BTW, what is good enough
> material to make mechanical/microscopy parts from?
>  
> We are expanding our Confocal Microscopy Core along with
> other Cores as we will be moving into a new research building,
> and I would like to start using 3D printer. So far on the listserv
> I found only mentioning of manufacturing some "crude boxes"
> http://derisilab.ucsf.edu/index.php?page=3D

I've used the Uprint printer mentioned in the Derisilab link for
printing a number of microscopy parts.  I've made adapters for the Nikon
condensor dovetail for mounting custom transillumination optics, filter
holders that slot into the Nikon filter turret for holding single
emission filters (these use a Thorlabs 1" tube to hold the filter), and
a large number of stage inserts and sample holders.  That Uprint printer
has about 200 um resolution so it's not great for printing really finely
detailed objects, but for these kinds of things it works great. It
prints ABS, which is pretty sturdy, and it also prints a dissolvable
support allowing for overhangs, windows, and nested objects.

One of these days I will post all of the CAD files we've generated....

Kurt

[Craig Brideau]

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On the high end, I have access to an Objet Connex500.  It has 15um
resolution (which is a bit insane) and prints in a wide variety of
materials.  The main drawback is the materials are all proprietary and a
bit expensive, but they do give very nice results.  We're working with the
biocompatible material (originally for dentistry) which has allowed us to
print some tissue hold-downs and cell chambers for ex vivo live imaging.
 I'll let you know how 'biocompatible' it turns out to be in the long run,
but so far we've had no issues with it for spinal cord and the like.

Craig


On Mon, Feb 18, 2013 at 10:58 AM, Kurt Thorn <[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>
> *****
>
> On 2/18/2013 8:08 AM, Arvydas Matiukas 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>
>> *****
>>
>> Dear list,
>>   Please share/advice what 3D printers you use to manufacture
>> parts for microscopy projects. BTW, what is good enough
>> material to make mechanical/microscopy parts from?
>>   We are expanding our Confocal Microscopy Core along with
>> other Cores as we will be moving into a new research building,
>> and I would like to start using 3D printer. So far on the listserv
>> I found only mentioning of manufacturing some "crude boxes"
>> http://derisilab.ucsf.edu/**index.php?page=3D<http://derisilab.ucsf.edu/index.php?page=3D>
>>
> I've used the Uprint printer mentioned in the Derisilab link for printing
> a number of microscopy parts.  I've made adapters for the Nikon condensor
> dovetail for mounting custom transillumination optics, filter holders that
> slot into the Nikon filter turret for holding single emission filters
> (these use a Thorlabs 1" tube to hold the filter), and a large number of
> stage inserts and sample holders.  That Uprint printer has about 200 um
> resolution so it's not great for printing really finely detailed objects,
> but for these kinds of things it works great. It prints ABS, which is
> pretty sturdy, and it also prints a dissolvable support allowing for
> overhangs, windows, and nested objects.
>
> One of these days I will post all of the CAD files we've generated....
>
> Kurt
>

[Armstrong, Brian]

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Craig, can you provide a rough estimate of what it costs in materials (and time) to operate this system?
Thanks,

Brian D Armstrong PhD
Assistant Research Professor
Director, Light Microscopy Core
Beckman Research Institute
City of Hope
Dept of Neuroscience
1450 E Duarte Rd
Duarte, CA 91010
626-256-4673 x62872



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Craig Brideau
Sent: Tuesday, February 19, 2013 1:00 PM
To: [hidden email]
Subject: Re: 3D printers for microscopy projects

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

On the high end, I have access to an Objet Connex500.  It has 15um
resolution (which is a bit insane) and prints in a wide variety of
materials.  The main drawback is the materials are all proprietary and a
bit expensive, but they do give very nice results.  We're working with the
biocompatible material (originally for dentistry) which has allowed us to
print some tissue hold-downs and cell chambers for ex vivo live imaging.
 I'll let you know how 'biocompatible' it turns out to be in the long run,
but so far we've had no issues with it for spinal cord and the like.

Craig


On Mon, Feb 18, 2013 at 10:58 AM, Kurt Thorn <[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>
> *****
>
> On 2/18/2013 8:08 AM, Arvydas Matiukas 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>
>> *****
>>
>> Dear list,
>>   Please share/advice what 3D printers you use to manufacture
>> parts for microscopy projects. BTW, what is good enough
>> material to make mechanical/microscopy parts from?
>>   We are expanding our Confocal Microscopy Core along with
>> other Cores as we will be moving into a new research building,
>> and I would like to start using 3D printer. So far on the listserv
>> I found only mentioning of manufacturing some "crude boxes"
>> http://derisilab.ucsf.edu/**index.php?page=3D<http://derisilab.ucsf.edu/index.php?page=3D>
>>
> I've used the Uprint printer mentioned in the Derisilab link for printing
> a number of microscopy parts.  I've made adapters for the Nikon condensor
> dovetail for mounting custom transillumination optics, filter holders that
> slot into the Nikon filter turret for holding single emission filters
> (these use a Thorlabs 1" tube to hold the filter), and a large number of
> stage inserts and sample holders.  That Uprint printer has about 200 um
> resolution so it's not great for printing really finely detailed objects,
> but for these kinds of things it works great. It prints ABS, which is
> pretty sturdy, and it also prints a dissolvable support allowing for
> overhangs, windows, and nested objects.
>
> One of these days I will post all of the CAD files we've generated....
>
> Kurt
>

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[Craig Brideau]

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The machine is about $200-250k I think.  The resin is $1300 to $1500 for a
3.6kg 'cartridge' of the biocompatible material.  The standard structural
material is around $1000 for the same mass.  We found that 3.6kg will
actually go quite a long way.  One catch; the material doesn't have a very
long shelf life so you have to use it within a couple months of purchase
for the biocompatible or about 6 months for the regular stuff.  As a
result, make sure you have all your designs and whatnot ready to go when
you place your order for the resin.  There's also a cleanout procedure you
have to do when switching materials which wastes a few hundred grams as you
have to rince the previous material out of the print heads with new stuff.
 You also need proper ventilation and power for the thing so budget for
some minor room renovations when you install the thing.  It has a huge
print tray though; it can print things the size of a medium-sized suitcase
if you want to use up that much material.  We'd regularly print 100 items
or so in a single run.  I've also used it to make optical mounts for PMTs
and other small mechanical parts in addition to the biocompatible chambers
and the like.  It works fairly well with Autodesk Inventor Professional,
which is free if you are a student/academic user.

Craig


On Tue, Feb 19, 2013 at 2:21 PM, Armstrong, Brian <[hidden email]>wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Craig, can you provide a rough estimate of what it costs in materials (and
> time) to operate this system?
> Thanks,
>
> Brian D Armstrong PhD
> Assistant Research Professor
> Director, Light Microscopy Core
> Beckman Research Institute
> City of Hope
> Dept of Neuroscience
> 1450 E Duarte Rd
> Duarte, CA 91010
> 626-256-4673 x62872
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Craig Brideau
> Sent: Tuesday, February 19, 2013 1:00 PM
> To: [hidden email]
> Subject: Re: 3D printers for microscopy projects
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> On the high end, I have access to an Objet Connex500.  It has 15um
> resolution (which is a bit insane) and prints in a wide variety of
> materials.  The main drawback is the materials are all proprietary and a
> bit expensive, but they do give very nice results.  We're working with the
> biocompatible material (originally for dentistry) which has allowed us to
> print some tissue hold-downs and cell chambers for ex vivo live imaging.
>  I'll let you know how 'biocompatible' it turns out to be in the long run,
> but so far we've had no issues with it for spinal cord and the like.
>
> Craig
>
>
> On Mon, Feb 18, 2013 at 10:58 AM, Kurt Thorn <[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>
> > *****
> >
> > On 2/18/2013 8:08 AM, Arvydas Matiukas 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>
> >> *****
> >>
> >> Dear list,
> >>   Please share/advice what 3D printers you use to manufacture
> >> parts for microscopy projects. BTW, what is good enough
> >> material to make mechanical/microscopy parts from?
> >>   We are expanding our Confocal Microscopy Core along with
> >> other Cores as we will be moving into a new research building,
> >> and I would like to start using 3D printer. So far on the listserv
> >> I found only mentioning of manufacturing some "crude boxes"
> >> http://derisilab.ucsf.edu/**index.php?page=3D<
> http://derisilab.ucsf.edu/index.php?page=3D>
> >>
> > I've used the Uprint printer mentioned in the Derisilab link for printing
> > a number of microscopy parts.  I've made adapters for the Nikon condensor
> > dovetail for mounting custom transillumination optics, filter holders
> that
> > slot into the Nikon filter turret for holding single emission filters
> > (these use a Thorlabs 1" tube to hold the filter), and a large number of
> > stage inserts and sample holders.  That Uprint printer has about 200 um
> > resolution so it's not great for printing really finely detailed objects,
> > but for these kinds of things it works great. It prints ABS, which is
> > pretty sturdy, and it also prints a dissolvable support allowing for
> > overhangs, windows, and nested objects.
> >
> > One of these days I will post all of the CAD files we've generated....
> >
> > Kurt
> >
>
>
> ---------------------------------------------------------------------
> *SECURITY/CONFIDENTIALITY WARNING:
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> entity to which they are addressed. This communication may contain
> information that is privileged, confidential, or exempt from disclosure
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> financial information). Because this e-mail has been sent without
> encryption, individuals other than the intended recipient may be able to
> view the information, forward it to others or tamper with the information
> without the knowledge or consent of the sender. If you are not the intended
> recipient, or the employee or person responsible for delivering the message
> to the intended recipient, any dissemination, distribution or copying of
> the communication is strictly prohibited. If you received the communication
> in error, please notify the sender immediately by replying to this message
> and deleting the message and any accompanying files from your system. If,
> due to the security risks, you do not wish to receive further
> communications via e-mail, please reply to this message and inform the
> sender that you do not wish to receive further e-mail from the sender.
> (fpc5p)
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>