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Automated tracking in Brightfield

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Claire Brown

Automated tracking in Brightfield

Does anyone have a program that does a good job tracking cells in brightfield (specifically phase contrast)? I know MetaMorph has a semi-manual tracking feature but I couldn’t seem to find it. If anyone knows where that function is in MetaMorph I would also appreciate it if you could let me know.

Sincerely,

Claire M. Brown, PhD

Life Sciences Complex Imaging Facility

McGill University

http://www.lifesciencescomplex.mcgill.ca/imaging

Jacqueline Ross

Re: Automated tracking in Brightfield

Hi Claire,

You can find Track Objects under Applications in MetaMorph. If you don’t see it there in your version of MM, then you might need to check that the Application is selected in Admin. I think it is a standard dropin though.

You can then use either a Template Match or Threshold. For phase contrast, you need to use Template Match. I have found it works quite well with rounded lymphocytes since the cell boundary is well defined. It’s easier with fluorescence images since you can use the threshold option.

There is a good document here from Molecular Devices: http://www.moleculardevices.com/pdfs2/MetaMatters_v1_i_4_FINAL.pdf which covers both Track Points and Track Objects.

Track Objects is covered from halfway down Page 3 of the document.

Kind regards,

Jacqui

Jacqueline Ross

Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: 64 9 373 7599 Ext 87438
Fax: 64 9 373 7484

http://www.fmhs.auckland.ac.nz/sms/biru/

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Claire Brown, Dr.
Sent: Wednesday, 27 January 2010 5:43 p.m.
To: [hidden email]
Subject: Automated tracking in Brightfield

Sincerely,

Claire M. Brown, PhD

Life Sciences Complex Imaging Facility

McGill University

http://www.lifesciencescomplex.mcgill.ca/imaging

Martin Spitaler

Re: Automated tracking in Brightfield

In reply to this post by Claire Brown

Dear Claire,

apply a Sobel or Kirsch filter to highlight edges. It converts all edges
into bright outlines on a dark background, so you can go on and use any
standard fluorescence tracking tool.
We have used it successfully in the C-Imaging / Hamamatsu SimplePCI
software, but they are established algorithms from photographic image
analysis (CCTV, satellite etc.), so it should be possible to find an
implementation in ImageJ or CellProfiler. Strange enough, they are still
rare in microscopy software.

Good luck,

Martin

On Tue, 26 Jan 2010 23:42:45 -0500, Claire Brown, Dr.
<[hidden email]> wrote:

>Does anyone have a program that does a good job tracking cells in
brightfield (specifically phase contrast)? I know MetaMorph has a
semi-manual tracking feature but I couldn't seem to find it. If anyone knows
where that function is in MetaMorph I would also appreciate it if you could
let me know.
>
>Sincerely,
>
>Claire M. Brown, PhD
>Life Sciences Complex Imaging Facility
>McGill University
>http://www.lifesciencescomplex.mcgill.ca/imaging
>
>

Keith Morris

Re: Automated tracking in Brightfield

In reply to this post by Claire Brown

Hi Claire,

Cell tracking:

These two applications should be under ‘Apps’ – as ‘Track Objects‘ [auto] or ‘Track Points’ [manual]. However you must have the Premiere version of MetaMorph not the Standard one [the Acquisition modules are irrelevant, the Apps are also available in MetaMorph Premiere Offline. From memory these apps are available in all versions of MetaMorph Premiere going back to at least v4.0.

Regards

Keith

---------------------------------------------------------------------------
Dr Keith J. Morris,
Molecular Cytogenetics and Microscopy Core,
Laboratory 00/069 and 00/070,
The Wellcome Trust Centre for Human Genetics,
Roosevelt Drive,
Oxford OX3 7BN,
United Kingdom.

Telephone: +44 (0)1865 287568
Email: [hidden email]

Web-pages: http://www.well.ox.ac.uk/molecular-cytogenetics-and-microscopy

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Claire Brown, Dr.
Sent: 27 January 2010 04:43
To: [hidden email]
Subject: Automated tracking in Brightfield

Sincerely,

Claire M. Brown, PhD

Life Sciences Complex Imaging Facility

McGill University

http://www.lifesciencescomplex.mcgill.ca/imaging

Beavers, Nick

Re: Automated tracking in Brightfield

**Commercial Employee Comment**

Hi Claire,

Nick Beavers here. In case you were wondering, tracking is one of Image-Pro Plus’ strengths and comes with every version, even the base package of Image-Pro. It can easily track in brightfield, phase, fluorescence, etc. If you can threshold your objects, or if they have a distinct morphological shape they can be tracked without incident. One method is AUTOMATIC, so all the objects can be tracked at once.

In case you’d like to see it in action, there is a brief 2D Tracking video on the website that I’ve linked below.

http://www.mediacy.com/Tutorials/2DTracking/2DTracking.html

Also know that 3D Tracking is also available and can be done automatically just like the 2D Tracking. No need to click every object at every frame, just choose the object your looking to track and it will be tracking in time and 3D space with annotations and thresholds.

I hope this helps!

Nick Beavers

Project Manager
Media Cybernetics, Inc.

4340 East-West hwy, Suite 400

Bethesda, MD 20814

m: 240.372.2171

o: 301.495.3305 x216

f: 301.495.5964

e: [hidden email]

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Keith Morris
Sent: Wednesday, January 27, 2010 4:56 AM
To: [hidden email]
Subject: Re: Automated tracking in Brightfield

Hi Claire,

Cell tracking:

Regards

Keith

Web-pages: http://www.well.ox.ac.uk/molecular-cytogenetics-and-microscopy

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Claire Brown, Dr.
Sent: 27 January 2010 04:43
To: [hidden email]
Subject: Automated tracking in Brightfield

Sincerely,

Claire M. Brown, PhD

Life Sciences Complex Imaging Facility

McGill University

http://www.lifesciencescomplex.mcgill.ca/imaging

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