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X-Y coordinates to pixels

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Leslie Day

X-Y coordinates to pixels

I am hoping someone could help me. I am trying to map a point as it moves
through a series of images in order to find out velocity of the object and
distance traveled.. I figured the best way would be to keep creating points
with the point selector and then map the points. However, currently when I
use the point selector it gives me x-y coordinates in whole numbers. I need
something with more significant figures (3 decimal spots) to be able to see
the movement. Maybe in pixels or μm. Perhaps there is another way to detect
linear velocity and distance traveled through a series of images.

Thanks

Leslie Day

Biology Department

Northeastern University

[hidden email]

617-373-3780

ctrueden

Re: X-Y coordinates to pixels

Hi Leslie,

I do not know if there is a way to measure points at higher precision in
ImageJ (though I would be surprised if there is not), but this is one of
the things VisBio (http://www.loci.wisc.edu/visbio/) can do. You can
place markers in double-precision floating point, and then export them
to a text file for use in a spreadsheet. See the Overlays page in the
"Data Transforms" section of the program's built-in help for details.

-Curtis

Leslie Day wrote:

>I am hoping someone could help me. I am trying to map a point as it moves
>through a series of images in order to find out velocity of the object and
>distance traveled.. I figured the best way would be to keep creating points
>with the point selector and then map the points. However, currently when I
>use the point selector it gives me x-y coordinates in whole numbers. I need
>something with more significant figures (3 decimal spots) to be able to see
>the movement. Maybe in pixels or μm. Perhaps there is another way to detect
>linear velocity and distance traveled through a series of images.
>
>
>
>Thanks
>
>
>
>Leslie Day
>
>Biology Department
>
>Northeastern University
>
>[hidden email]
>
>617-373-3780
>
>

Liu, Dongfang (NIH/NIAID) [F]

Re: X-Y coordinates to pixels

In reply to this post by Leslie Day

Dear Sir,

I have the same problem. Could I calculate the displacement of two particles according to the pixel size?

**********************************************
Dongfang Liu
Laboratory of Immunogenetics
National Institute of Allergy and Infectious Disease
National Institute of Health
Twinbrook II, Room 207
12441 Parklawn Drive
Rockville, MD 20852
Phone: 301-496-2951
Fax:301-402-0259
email:[hidden email]
**********************************************

> ----------
> From: Curtis Rueden
> Reply To: List IMAGEJ
> Sent: Wednesday, February 1, 2006 3:20 PM
> To: List IMAGEJ
> Subject: Re: X-Y coordinates to pixels
>
> Hi Leslie,
>
> I do not know if there is a way to measure points at higher precision in
> ImageJ (though I would be surprised if there is not), but this is one of
> the things VisBio (http://www.loci.wisc.edu/visbio/) can do. You can
> place markers in double-precision floating point, and then export them
> to a text file for use in a spreadsheet. See the Overlays page in the
> "Data Transforms" section of the program's built-in help for details.
>
> -Curtis
>
> Leslie Day wrote:
>
> >I am hoping someone could help me. I am trying to map a point as it moves
> >through a series of images in order to find out velocity of the object and
> >distance traveled.. I figured the best way would be to keep creating points
> >with the point selector and then map the points. However, currently when I
> >use the point selector it gives me x-y coordinates in whole numbers. I need
> >something with more significant figures (3 decimal spots) to be able to see
> >the movement. Maybe in pixels or ?m. Perhaps there is another way to detect
> >linear velocity and distance traveled through a series of images.
> >
> >
> >
> >Thanks
> >
> >
> >
> >Leslie Day
> >
> >Biology Department
> >
> >Northeastern University
> >
> >[hidden email]
> >
> >617-373-3780
> >
> >
>

Michael Cammer

Re: X-Y coordinates to pixels

To measure particles, either you need to do it per pixel which, by
definition, is a discrete number, or you need to look at a block of pixels
and do a gaussian or other fit if you need to find a fraction of a pixel
location.
-mc

At 09:14 AM 02/02/06 -0500, you wrote:

>Dear Sir,
>
>I have the same problem. Could I calculate the displacement of two
>particles according to the pixel size?
>
>
>
>
>
>
>
>**********************************************
>Dongfang Liu
>Laboratory of Immunogenetics
>National Institute of Allergy and Infectious Disease
>National Institute of Health
>Twinbrook II, Room 207
>12441 Parklawn Drive
>Rockville, MD 20852
>Phone: 301-496-2951
>Fax:301-402-0259
>email:[hidden email]
>**********************************************
>
> > ----------
> > From: Curtis Rueden
> > Reply To: List IMAGEJ
> > Sent: Wednesday, February 1, 2006 3:20 PM
> > To: List IMAGEJ
> > Subject: Re: X-Y coordinates to pixels
> >
> > Hi Leslie,
> >
> > I do not know if there is a way to measure points at higher precision in
> > ImageJ (though I would be surprised if there is not), but this is one of
> > the things VisBio (http://www.loci.wisc.edu/visbio/) can do. You can
> > place markers in double-precision floating point, and then export them
> > to a text file for use in a spreadsheet. See the Overlays page in the
> > "Data Transforms" section of the program's built-in help for details.
> >
> > -Curtis
> >
> > Leslie Day wrote:
> >
> > >I am hoping someone could help me. I am trying to map a point as it moves
> > >through a series of images in order to find out velocity of the object and
> > >distance traveled.. I figured the best way would be to keep creating
> points
> > >with the point selector and then map the points. However, currently when I
> > >use the point selector it gives me x-y coordinates in whole numbers. I
> need
> > >something with more significant figures (3 decimal spots) to be able
> to see
> > >the movement. Maybe in pixels or ?m. Perhaps there is another way to
> detect
> > >linear velocity and distance traveled through a series of images.
> > >
> > >
> > >
> > >Thanks
> > >
> > >
> > >
> > >Leslie Day
> > >
> > >Biology Department
> > >
> > >Northeastern University
> > >
> > >[hidden email]
> > >
> > >617-373-3780
> > >
> > >
> >

____________________________________________________________________________
Michael Cammer Analytical Imaging Facility Albert Einstein Coll. of Med.
Jack & Pearl Resnick Campus 1300 Morris Park Ave. Bronx, NY 10461
(718) 430-2890 Fax: 430-8996 URL: http://www.aecom.yu.edu/aif/
**This electronic transmission contains information that is privileged.**

Liu, Dongfang (NIH/NIAID) [F]

Re: X-Y coordinates to pixels

In reply to this post by Leslie Day

Dear Sir,

Could you do it in Image Pro or Image J? How to do 2-Dimension Gauss Fit(for a fluorescence spot)?

> ----------
> From: Michael Cammer
> Reply To: List IMAGEJ
> Sent: Thursday, February 2, 2006 9:36 AM
> To: List IMAGEJ
> Subject: Re: X-Y coordinates to pixels
>
> To measure particles, either you need to do it per pixel which, by
> definition, is a discrete number, or you need to look at a block of pixels
> and do a gaussian or other fit if you need to find a fraction of a pixel
> location.
> -mc
>
>
>
> At 09:14 AM 02/02/06 -0500, you wrote:
> >Dear Sir,
> >
> >I have the same problem. Could I calculate the displacement of two
> >particles according to the pixel size?
> >
> >
> >
> >
> >
> >
> >
> >**********************************************
> >Dongfang Liu
> >Laboratory of Immunogenetics
> >National Institute of Allergy and Infectious Disease
> >National Institute of Health
> >Twinbrook II, Room 207
> >12441 Parklawn Drive
> >Rockville, MD 20852
> >Phone: 301-496-2951
> >Fax:301-402-0259
> >email:[hidden email]
> >**********************************************
> >
> > > ----------
> > > From: Curtis Rueden
> > > Reply To: List IMAGEJ
> > > Sent: Wednesday, February 1, 2006 3:20 PM
> > > To: List IMAGEJ
> > > Subject: Re: X-Y coordinates to pixels
> > >
> > > Hi Leslie,
> > >
> > > I do not know if there is a way to measure points at higher precision in
> > > ImageJ (though I would be surprised if there is not), but this is one of
> > > the things VisBio (http://www.loci.wisc.edu/visbio/) can do. You can
> > > place markers in double-precision floating point, and then export them
> > > to a text file for use in a spreadsheet. See the Overlays page in the
> > > "Data Transforms" section of the program's built-in help for details.
> > >
> > > -Curtis
> > >
> > > Leslie Day wrote:
> > >
> > > >I am hoping someone could help me. I am trying to map a point as it moves
> > > >through a series of images in order to find out velocity of the object and
> > > >distance traveled.. I figured the best way would be to keep creating
> > points
> > > >with the point selector and then map the points. However, currently when I
> > > >use the point selector it gives me x-y coordinates in whole numbers. I
> > need
> > > >something with more significant figures (3 decimal spots) to be able
> > to see
> > > >the movement. Maybe in pixels or ?m. Perhaps there is another way to
> > detect
> > > >linear velocity and distance traveled through a series of images.
> > > >
> > > >
> > > >
> > > >Thanks
> > > >
> > > >
> > > >
> > > >Leslie Day
> > > >
> > > >Biology Department
> > > >
> > > >Northeastern University
> > > >
> > > >[hidden email]
> > > >
> > > >617-373-3780
> > > >
> > > >
> > >
>
> ____________________________________________________________________________
> Michael Cammer Analytical Imaging Facility Albert Einstein Coll. of Med.
> Jack & Pearl Resnick Campus 1300 Morris Park Ave. Bronx, NY 10461
> (718) 430-2890 Fax: 430-8996 URL: http://www.aecom.yu.edu/aif/
> **This electronic transmission contains information that is privileged.**
>
>

Leslie Day

Re: X-Y coordinates to pixels

In reply to this post by Michael Cammer

Okay. Then I rephrase my question... How can I get image J to give me
another measurement of a point, besides pixels. Some that is much more
precise and can help me measure small amounts of movement?

I am not sure what a Gaussian is.

Leslie Day
Biology Department
Northeastern University
[hidden email]
617-373-3780

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Michael Cammer
Sent: Thursday, February 02, 2006 9:37 AM
To: [hidden email]
Subject: Re: X-Y coordinates to pixels

To measure particles, either you need to do it per pixel which, by
definition, is a discrete number, or you need to look at a block of pixels
and do a gaussian or other fit if you need to find a fraction of a pixel
location.
-mc

At 09:14 AM 02/02/06 -0500, you wrote:

moves
> > >through a series of images in order to find out velocity of the object
and
> > >distance traveled.. I figured the best way would be to keep creating
> points
> > >with the point selector and then map the points. However, currently
when I

> > >use the point selector it gives me x-y coordinates in whole numbers. I
> need
> > >something with more significant figures (3 decimal spots) to be able
> to see
> > >the movement. Maybe in pixels or ?m. Perhaps there is another way to
> detect
> > >linear velocity and distance traveled through a series of images.
> > >
> > >
> > >
> > >Thanks
> > >
> > >
> > >
> > >Leslie Day
> > >
> > >Biology Department
> > >
> > >Northeastern University
> > >
> > >[hidden email]
> > >
> > >617-373-3780
> > >
> > >
> >

Gabriel Landini

Re: X-Y coordinates to pixels

On Friday 03 February 2006 14:12, Leslie Day wrote:
> Okay. Then I rephrase my question... How can I get image J to give me
> another measurement of a point, besides pixels. Some that is much more
> precise and can help me measure small amounts of movement?

One cannot draw ROI with sub-pixel accuracy in ImageJ.
Even if one could, I guess that it would be difficult to argue that one can
consistently do it, or that there is really an advantage, given that the data
one has to analyze has a coarser resolution than the ROI one is defining.
Instead, it is better and easier to obtain images with more resolution.

> I am not sure what a Gaussian is.

It is a function that describes a special type of distribution (actually one
of the most important ones in science). It would be very useful to find out
about this, specially if you are thinking of doing any statistical analysis.

Cheers,

Gabriel