Tracking cells automatically during a long time-lapse experimnet

[Romin, Yevgeniy/Sloan Kettering Institute]

Dear List

 

I have another question about live imaging, since all of you have been so helpful with your responses before.  We are planning on running an experiment where we want to follow a cell that will be moving quite a lot over an extended period of time.  We need to somehow keep this cell in the field of view throughout the whole experiment.  The two possibilities that come to mind are either taking a relatively large tilescan at every timepoint and hope that the cell will not go past the area, or writing a lengthy and complex journal in a program like Metamorph in order to detect the cells movement within the field and move the stage with it over time.  Has anyone done a similar experiment?  Are there any commercial systems available that are able to do this?

 

Thanks very much to everybody in advance,

 

---------------------------------------------------

Yevgeniy Romin

 

Digital Microscopist

Memorial Sloan-Kettering Cancer Center

Molecular Cytology Core Facility

1275 York Ave. Box 333

New York, NY 10065

Tel.[phone]

Fax. [phone]

---------------------------------------------------

 

 
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[Martin Wessendorf-2]

Dear Yevgeniy--

If I remember correctly, Keith Lidke in the Physics Dept at University
of New Mexico has written a MatLab script that can move the stage to
keep a particle in the middle of a field of view.  Not sure whether or
not that would work with a cell but you might want to contact him and check.

Good luck--

Martin Wessendorf

Yevgeniy Romin wrote:

> Dear List
>
>  
>
> I have another question about live imaging, since all of you have been
> so helpful with your responses before.  We are planning on running an
> experiment where we want to follow a cell that will be moving quite a
> lot over an extended period of time.  We need to somehow keep this cell
> in the field of view throughout the whole experiment.  The two
> possibilities that come to mind are either taking a relatively large
> tilescan at every timepoint and hope that the cell will not go past the
> area, or writing a lengthy and complex journal in a program like
> Metamorph in order to detect the cells movement within the field and
> move the stage with it over time.  Has anyone done a similar
> experiment?  Are there any commercial systems available that are able to
> do this?
>
>  
>
> Thanks very much to everybody in advance,
>
>  
>
> ---------------------------------------------------
>
> *Yevgeniy Romin*

--
Martin Wessendorf, Ph.D.                   office: [phone]
Assoc Prof, Dept Neuroscience                 lab: [phone]
University of Minnesota             Preferred FAX: [phone]
6-145 Jackson Hall, 321 Church St. SE    Dept Fax: [phone]
Minneapolis, MN  55455                    e-mail: [hidden email]

[lechristophe]

Dear Yevgeniy,

You should have a look at J. Ellenberg's paper that has done automatic
cell tracking using Zeiss LSM software to keep a cell at the center of
the field of view :

Rabut G, Ellenberg J. Automatic real-time three-dimensional cell tracking by
fluorescence microscopy. J Microsc. 2004 Nov;216(Pt 2):131-7. PubMed PMID:
15516224.
http://www3.interscience.wiley.com/journal/118757070/abstract


Christophe


On Wed, May 5, 2010 at 17:55, Martin Wessendorf <[hidden email]> wrote:

>
> Dear Yevgeniy--
>
> If I remember correctly, Keith Lidke in the Physics Dept at University of New Mexico has written a MatLab script that can move the stage to keep a particle in the middle of a field of view.  Not sure whether or not that would work with a cell but you might want to contact him and check.
>
> Good luck--
>
> Martin Wessendorf
>
> Yevgeniy Romin wrote:
>>
>> Dear List
>>
>>
>> I have another question about live imaging, since all of you have been so helpful with your responses before.  We are planning on running an experiment where we want to follow a cell that will be moving quite a lot over an extended period of time.  We need to somehow keep this cell in the field of view throughout the whole experiment.  The two possibilities that come to mind are either taking a relatively large tilescan at every timepoint and hope that the cell will not go past the area, or writing a lengthy and complex journal in a program like Metamorph in order to detect the cells movement within the field and move the stage with it over time.  Has anyone done a similar experiment?  Are there any commercial systems available that are able to do this?
>>
>>
>> Thanks very much to everybody in advance,
>>
>>
>> ---------------------------------------------------
>>
>> *Yevgeniy Romin*
>
> --
> Martin Wessendorf, Ph.D.                   office: [phone]
> Assoc Prof, Dept Neuroscience                 lab: [phone]
> University of Minnesota             Preferred FAX: [phone]
> 6-145 Jackson Hall, 321 Church St. SE    Dept Fax: [phone]
> Minneapolis, MN  55455                    e-mail: [hidden email]

[Vincent Schoonderwoert]

*commercial interest*

Dear Yevgeniy,

A few months ago, we have released the Object Stabilizer for our Huygens software.
This new tool measures and corrects for cell motion, thermal drift, shaking, and other types of movement (x-y-z translation and axial rotation). Both the measurement and subsequent stabilization are done in 3D and at sub-pixel level. The Stabilizer not only stabilizes 2D or 3D time series, but it also allows the alignment of slices within a 3D stack.
An example movie of a stabilized image can be viewed on our homepage.
You can use the link on this website for a free trial version.

Best regards,
Vincent
Scientific Volume Imaging bv.
http://www.svi.nl
[hidden email]


We have have released a few months ago the

2010/5/5 Yevgeniy Romin <[hidden email]>

Dear List

 

I have another question about live imaging, since all of you have been so helpful with your responses before.  We are planning on running an experiment where we want to follow a cell that will be moving quite a lot over an extended period of time.  We need to somehow keep this cell in the field of view throughout the whole experiment.  The two possibilities that come to mind are either taking a relatively large tilescan at every timepoint and hope that the cell will not go past the area, or writing a lengthy and complex journal in a program like Metamorph in order to detect the cells movement within the field and move the stage with it over time.  Has anyone done a similar experiment?  Are there any commercial systems available that are able to do this?

 

Thanks very much to everybody in advance,

 

---------------------------------------------------

Yevgeniy Romin

 

Digital Microscopist

Memorial Sloan-Kettering Cancer Center

Molecular Cytology Core Facility

1275 York Ave. Box 333

New York, NY 10065

Tel.[phone]

Fax. [phone]

---------------------------------------------------

 

 
     =====================================================================
     
     Please note that this e-mail and any files transmitted with it may be 
     privileged, confidential, and protected from disclosure under 
     applicable law. If the reader of this message is not the intended 
     recipient, or an employee or agent responsible for delivering this 
     message to the intended recipient, you are hereby notified that any 
     reading, dissemination, distribution, copying, or other use of this 
     communication or any of its attachments is strictly prohibited.  If 
     you have received this communication in error, please notify the 
     sender immediately by replying to this message and deleting this 
     message, any attachments, and all copies and backups from your 
     computer.

[Nico Stuurman]

I have another question about live imaging, since all of you have been so helpful with your responses before.  We are planning on running an experiment where we want to follow a cell that will be moving quite a lot over an extended period of time.  We need to somehow keep this cell in the field of view throughout the whole experiment.  The two possibilities that come to mind are either taking a relatively large tilescan at every timepoint and hope that the cell will not go past the area, or writing a lengthy and complex journal in a program like Metamorph in order to detect the cells movement within the field and move the stage with it over time.  Has anyone done a similar experiment?  Are there any commercial systems available that are able to do this?

The non-commercial (free) Micro-Manager software ( http://micro-manager.org ) includes the "Tracker" plugin that keeps moving cells centered in the image by moving the stage to correct for cell movement.  It was build and tested to track moving keratocytes.  As it uses cross-correlation between images it is likely to work with most other moving objects as well.  Micro-Manager works with most microscope hardware components.

Best,

Nico

 

[Donnelly, Tom]

Nico;

 

Since the release of the RT version about five years ago all DeltaVision systems have been able to track cell movement and return the target to the center of the field of view.

 

The user selects a ROI and chooses to track either center of mass or center of intensity.  The user then selects a threshold distance.  When the ROI reaches the threshold the XYZ stage returns the target to the center of the field of view and records new X-Y coordinates.

 

This process works equally well for single and multi-point visiting experiments.

 

Cheers,

 

Tom Donnelly

www.appliedprecision.com

---

From: Nico Stuurman [mailto:[hidden email]]
Sent: Saturday, May 08, 2010 9:28 AM
To: [hidden email]
Subject: Re: Tracking cells automatically during a long time-lapse experimnet

I have another question about live imaging, since all of you have been so helpful with your responses before.  We are planning on running an experiment where we want to follow a cell that will be moving quite a lot over an extended period of time.  We need to somehow keep this cell in the field of view throughout the whole experiment.  The two possibilities that come to mind are either taking a relatively large tilescan at every timepoint and hope that the cell will not go past the area, or writing a lengthy and complex journal in a program like Metamorph in order to detect the cells movement within the field and move the stage with it over time.  Has anyone done a similar experiment?  Are there any commercial systems available that are able to do this?

The non-commercial (free) Micro-Manager software ( http://micro-manager.org ) includes the "Tracker" plugin that keeps moving cells centered in the image by moving the stage to correct for cell movement.  It was build and tested to track moving keratocytes.  As it uses cross-correlation between images it is likely to work with most other moving objects as well.  Micro-Manager works with most microscope hardware components.

Best,

Nico

This email message, together with any attachments, is for the sole use of the intended recipient(s) and is the confidential information of Applied Precision Inc. If you are not the intended recipient, your review, use, disclosure, copying or dissemination of this email message or its attachments, or the information contained therein, is strictly prohibited. If you are not the intended recipient or if you think this email was sent to you in error, please notify the sender by reply email and delete this message and its attachments, as well as all copies, from your system.

[Donnelly, Tom]

Nico;

 

I apologize.  I did not notice the first paragraph was from another post.

 

Tom

---

From: Nico Stuurman [mailto:[hidden email]]
Sent: Saturday, May 08, 2010 9:28 AM
To: [hidden email]
Subject: Re: Tracking cells automatically during a long time-lapse experimnet

I have another question about live imaging, since all of you have been so helpful with your responses before.  We are planning on running an experiment where we want to follow a cell that will be moving quite a lot over an extended period of time.  We need to somehow keep this cell in the field of view throughout the whole experiment.  The two possibilities that come to mind are either taking a relatively large tilescan at every timepoint and hope that the cell will not go past the area, or writing a lengthy and complex journal in a program like Metamorph in order to detect the cells movement within the field and move the stage with it over time.  Has anyone done a similar experiment?  Are there any commercial systems available that are able to do this?

The non-commercial (free) Micro-Manager software ( http://micro-manager.org ) includes the "Tracker" plugin that keeps moving cells centered in the image by moving the stage to correct for cell movement.  It was build and tested to track moving keratocytes.  As it uses cross-correlation between images it is likely to work with most other moving objects as well.  Micro-Manager works with most microscope hardware components.

Best,

Nico

This email message, together with any attachments, is for the sole use of the intended recipient(s) and is the confidential information of Applied Precision Inc. If you are not the intended recipient, your review, use, disclosure, copying or dissemination of this email message or its attachments, or the information contained therein, is strictly prohibited. If you are not the intended recipient or if you think this email was sent to you in error, please notify the sender by reply email and delete this message and its attachments, as well as all copies, from your system.

[Alberto Diaspro]

Dear friends,
a reminder for two Microscopy Schools, one - practical -  in Genoa from June 21 to 23 on Confocal-Multiphoton-Superresolution and a second one, a Course, in Varenna on the Como lake from July 12 to 17 on Advanced Microscopy and Nanoscopy.
Deadline is approaching fast, last remaining seats available. For the first one, please send an email to [hidden email] - subject: Genoa School 2010, for the second one you can find more details on www.sif.it, please send an email to [hidden email] - subject: Varenna Course 2010.
See you in Italy this Summer.
All the best
Alby




ISTITUTO ITALIANO
DI TECNOLOGIA
 
Prof. Alberto Diaspro
Scientific Head
Nanophysics
Via Morego, 30 16163 Genova
Tel: [phone]
Fax [phone]
Mobile [phone]
www.iit.it
[hidden email]

 

[Cameron Nowell]

Hi Nico,
 
I would have thought that the journal for MetaMorph woudln't be that complex. All you need to do is get the X,Y co-ordinates variable of the object you are interested, measure the diference in them each time point and add (or subtract) that difference from the stage X,Y co-ordinates variable. Of course this could get a bit tricky if there were too many cells in each field.
 
Feel free to contact me off list if you want any help putting the journal together.
 
 
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 Nico Stuurman
Sent: Sun 9/05/2010 2:27 AM
To: [hidden email]
Subject: Re: Tracking cells automatically during a long time-lapse experimnet



       
        I have another question about live imaging, since all of you have been so helpful with your responses before.  We are planning on running an experiment where we want to follow a cell that will be moving quite a lot over an extended period of time.  We need to somehow keep this cell in the field of view throughout the whole experiment.  The two possibilities that come to mind are either taking a relatively large tilescan at every timepoint and hope that the cell will not go past the area, or writing a lengthy and complex journal in a program like Metamorph in order to detect the cells movement within the field and move the stage with it over time.  Has anyone done a similar experiment?  Are there any commercial systems available that are able to do this?


The non-commercial (free) Micro-Manager software ( http://micro-manager.org <http://micro-manager.org/>  ) includes the "Tracker" plugin that keeps moving cells centered in the image by moving the stage to correct for cell movement.  It was build and tested to track moving keratocytes.  As it uses cross-correlation between images it is likely to work with most other moving objects as well.  Micro-Manager works with most microscope hardware components.

Best,

Nico