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Tracking with Metamorph

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Nishigandha Naik

Tracking with Metamorph

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Dear All,

We are trying to analyze cell motility using Metamorph
software. We could not find the way to measure the net
displacement of the cell, i.e., the straight line
distance between the first point to the last point of
the cell track traced. I will be thankful if anybody
could help.

Regards,

Nishigandha Naik

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Scott Howell-3

Re: Tracking with Metamorph

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Nishigandha,

If you go into Metamorph and go under the APPS tab you MAY have a
track objects selection. If you do open it up, hit F1 and follow the
instructions. Of course Metamorph is very modular and you may not own
this particular application. If you have any questions feel free to
contact me off list. Good Luck.

Scott J. Howell, Ph.D.
Manager, Imaging Module
Visual Sciences Research Center
Case Western Reserve University
2085 Adelbert Rd.
Institute of Pathology Room 106
Cleveland, Ohio 44106
216-368-2300
http://www.case.edu/med/vsrc/

----- Original Message -----
From: Nishigandha Naik <[hidden email]>
Date: Thursday, August 16, 2007 7:42 am
Subject: Tracking with Metamorph
To: [hidden email]

Hugo.Ostermann

AW: Tracking with Metamorph

In reply to this post by Nishigandha Naik

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Dear Nishigandha Nai

maybe you can find a copy of Image Pro Plus from Media Cybernetics. It
includes a very powerful tracking module which calculates not only the
distance travelled but also the shortest distance between start- and
endpoint

Mit freundlichen Grüßen,

Hugo Ostermann

CHROMAPHOR Analysen-Technik GmbH
Mühlenkamp 37
D-59387 Ascheberg - Germany
Tel: ++49 - 2593-928.600
Fax: ++49 - 2593-928.601
mail: [hidden email]
URL: http://www.chromaphor.de

-----Ursprüngliche Nachricht-----
Von: Confocal Microscopy List [mailto:[hidden email]] Im
Auftrag von Nishigandha Naik
Gesendet: Donnerstag, 16. August 2007 13:42
An: [hidden email]
Betreff: Tracking with Metamorph

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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear All,

We are trying to analyze cell motility using Metamorph
software. We could not find the way to measure the net
displacement of the cell, i.e., the straight line
distance between the first point to the last point of
the cell track traced. I will be thankful if anybody
could help.

Regards,

Nishigandha Naik

____________________________________________________________________________
________
Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail,
news, photos & more.
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Nowell, Cameron

Re: Tracking with Metamorph

In reply to this post by Scott Howell-3

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Howdy,
You may not see the application you need in the apps menu, but
this does not mean that you do not have the module availible to install.
If you log into the admin part of metamorph and find the dropins
configuration settings. In there you can turn on and off any of the
modules you have available.

Cam

Cameron Nowell B.Sc (Hons)

Microscopy Imaging and Research Core Facility
Peter MacCallum Cancer Centre
7 St Andrews Place
East Melbourne, Victoria 3002

Phone: +61396561243
Mobile: +61422882700
Fax: +61396561411

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Scott Howell
Sent: Thursday, 16 August 2007 11:22 PM
To: [hidden email]
Subject: Re: Tracking with Metamorph

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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Nishigandha,

If you go into Metamorph and go under the APPS tab you MAY have a track
objects selection. If you do open it up, hit F1 and follow the
instructions. Of course Metamorph is very modular and you may not own
this particular application. If you have any questions feel free to
contact me off list. Good Luck.

Scott J. Howell, Ph.D.
Manager, Imaging Module
Visual Sciences Research Center
Case Western Reserve University
2085 Adelbert Rd.
Institute of Pathology Room 106
Cleveland, Ohio 44106
216-368-2300
http://www.case.edu/med/vsrc/

----- Original Message -----
From: Nishigandha Naik <[hidden email]>
Date: Thursday, August 16, 2007 7:42 am
Subject: Tracking with Metamorph
To: [hidden email]

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Dear All,
>
> We are trying to analyze cell motility using Metamorph software. We
> could not find the way to measure the net displacement of the cell,
> i.e., the straight line distance between the first point to the last
> point of the cell track traced. I will be thankful if anybody could
> help.
>
> Regards,
>
> Nishigandha Naik
>
>
>
>
>

_______________________________________________________________________
_____________
> Take the Internet to Go: Yahoo!Go puts the Internet in your
> pocket: mail, news, photos & more.
> http://mobile.yahoo.com/go?refer=1GNXIC
>

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heckman@bgnet.bgsu.edu

Re: Tracking with Metamorph

In reply to this post by Nishigandha Naik

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Dear Nishigandha-
If you can get MetaMorph to segment the cell boundary, even if it is
not perfect, it can then be instructed to calculate the centroid
positions. These are the x,y coordinates of the ellipse of
concentration of the segmented figure. The Euclidean distance
between any two centroids is a fair measure of the net displacement
of the cell. This is if you are working on a two-dimensional plane.
In three dimensions, you would have to take the z dimension into
account.
Carol

>Search the CONFOCAL archive at
>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>Dear All,
>
>We are trying to analyze cell motility using Metamorph
>software. We could not find the way to measure the net
>displacement of the cell, i.e., the straight line
>distance between the first point to the last point of
>the cell track traced. I will be thankful if anybody
>could help.
>
>Regards,
>
>Nishigandha Naik
>
>
>
>
>____________________________________________________________________________________
>Take the Internet to Go: Yahoo!Go puts the Internet in your pocket:
>mail, news, photos & more.
>http://mobile.yahoo.com/go?refer=1GNXIC

--
Carol A. Heckman, Ph.D.
Director, Center for Microscopy & Microanalysis
and Professor of Biological Sciences
Bowling Green State University
Bowling Green, OH 43403
USA
website: http://www.bgsu.edu/departments/biology/facilities/MnM

George McNamara

Re: Tracking with Metamorph

In reply to this post by Nishigandha Naik

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Apps menu - Track Objects. As pointed out by another poster, you may
need to run MM Admin and add the dropin. See the MetaMorph help file
for information about the command. It was developed for Single
Particle Tracking (i.e. small blobs in DIC).

Another Apps menu item is Track Points, which makes it easy to do
manual tracks, analysis and graphs (always good to verify what is
going on). You can also do this with "Measure Pixels". Just go to the
first plane, click on the object to log the data (if you have the
data log open and MP dialog open), then last plane, click, Publish.

If you decide you want entire tracks, and have only one or a few
cells in a stack, and they are easily thresholded (for example, 0.1
ug/mL Hoechst or DAPI fluorescent DNA counterstained nuclei), you can
use Integrated Morphometry Analysis / Measure Objects with "loop for
all planes". I prefer Measure Objects (legacy dropin measobj), set up
threshold, classifier(s), measurements (at least X, Y, plane!), and
set up the inner loop journal to add the measured result image into
the bottom of a stack. If you have "show centroid" on (Preferences),
you will get a set of images that have the object(s) with their
centroids highlighted.

Hint: I recommend NOT doing "calibrate distances" (Measure menu).
Easier to log the raw image data - pixels - to Excel, understand the
data, then convert from pixels to um at the end. If you are not
rigorous about applying calibrate distances, some images may be in um
(or lightyears, etc) and others may be pixels.

If your cells have high contrast (i.e. fluorescent nuclei) you can
use Process menu: Stack Arithmetic: Max, so see all pixels covered
("temporal area maps" see
http://home.earthlink.net/~geomcnamara/temporal_area_maps.htm I
typically make a binary stack first, then do TAM). You can likewise
use Stack menu: Topographic Surface Maps, to see first time point
covered. If you make the TAM map, you may be able to put a line ROI
on the beginning and end of the track, and use the Measure Regions
table to get the distance you want.

Your friendly neighborhood MetaMorph sales rep can show you how to do
all these items. you can also call UIC/MDS/MDS for help.

best wishes,

George

At 07:41 AM 8/16/2007, you wrote:

George McNamara, Ph.D.
University of Miami, Miller School of Medicine
Image Core
Miami, FL 33010
[hidden email]
[hidden email]
305-243-8436 office