sperm head area

[Somporn Duanyai]

Dear all,

Please advise me how to use Image j for measuring sperm head area.

Kindest regards.

somporn duanyai

[lechristophe]

With that subject and your first name (with all due respect), beware of
anti-spam protections ;)

Joke appart, if the "head" is a round feature, try "Analyze Particles"
with a circularity close to 1. It would be much better to host one of
your image somewhere on the web and give us the link to see what you're
talking about.

Best Regards, and happy new year everybody

Christophe



Somporn Duanyai wrote:
> Dear all,
>
> Please advise me how to use Image j for measuring sperm head area.
>
> Kindest regards.
>
> somporn duanyai
>


--
Christophe Leterrier

Postdoc
INSERM UMR641 Neurobiology of ionic channels
IFR Jean Roche - Mediterranee University
Marseille, France

[Martin Wessendorf]

Somporn Duanyai wrote:

> Please advise me how to use Image j for measuring sperm head area.

What do you mean by the "sperm head area"?  The surface area?  Or the
cross-sectional area?

In either case, the answer that you obtain may depend as much on optical
and stereological issues as it does on the specific method you use.
Different species have different sized sperm heads; some are so small
that it could be challenging to obtain an accurate measurement by
optical microscopy.

The stereological issues are outlined in CV Howard and MG Reed's book,
"Unbiased Stereology".  If you haven't already, consult that or a
similar book before you go too much further.

Good luck!

Martin Wessendorf
--
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: martinw[at]med.umn.edu

[David Finkelstein-2]

Hi Image J ers,
Are there any Stereology plug ins for Image J.
Specifically, an ability to drop\superimpose a counting frame (of user
defined size and step size) onto a section image.  Then the ability to zoom
into each of the counting frames in order.
Regards
David

David Finkelstein (PhD),
The Mental Health Research Institute of Victoria,
155 Oak Street, Parkville, Victoria 3052
AUSTRALIA
-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Martin
Wessendorf
Sent: Friday, 5 January 2007 5:14 AM
To: [hidden email]
Subject: Re: sperm head area

Somporn Duanyai wrote:

> Please advise me how to use Image j for measuring sperm head area.

What do you mean by the "sperm head area"?  The surface area?  Or the
cross-sectional area?

In either case, the answer that you obtain may depend as much on optical
and stereological issues as it does on the specific method you use.
Different species have different sized sperm heads; some are so small
that it could be challenging to obtain an accurate measurement by
optical microscopy.

The stereological issues are outlined in CV Howard and MG Reed's book,
"Unbiased Stereology".  If you haven't already, consult that or a
similar book before you go too much further.

Good luck!

Martin Wessendorf
--
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: martinw[at]med.umn.edu

[Martin Wessendorf]

David Finkelstein wrote:

> Are there any Stereology plug ins for Image J.
> Specifically, an ability to drop\superimpose a counting frame (of user
> defined size and step size) onto a section image.  Then the ability to zoom
> into each of the counting frames in order.

There's the "grid" plugin ("Draw line or point grids":
http://rsb.info.nih.gov/ij/plugins/grid.html).  It's good for randomly
creating a grid over an image, e.g. for cavalieri estimations of volume
or to create a random set of points for systematic random sampling.

For a counting frame, we simply draw one on a piece of acetate that we
tape to the computer monitor.  Very low-tech but it works.

The "IJStage and IJSerial (microscope stage control and serial I/O)"
plugin (http://www.eslide.net/ijstage.php) appears able to control some
types of stages but you'd need to program in the specifics for
systematic random sampling.

Good luck--

Martin Wessendorf

--
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: martinw[at]med.umn.edu

[Jacqueline Ross]

Dear All,

Since Martin has mentioned the Grid plugin which works well for
systematic sampling, can anyone remind me how you designate the size of
the grid relative to your image field that you should use for sampling
for manual counting, etc.?

There's also a macro called DrawRandomDots that seems to follow the
Chalkley Grid method and draws 25 random dots on the image. Can anyone
tell me if the dots are programmed to be the correct size for sampling
relative to any image?

Cheers,

Jacqui.

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

Tel: [phone] Ext 87438
Fax: [phone]

http://www.health.auckland.ac.nz/biru/ 

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Martin Wessendorf
Sent: 05 January 2007 09:32
To: [hidden email]
Subject: Re: Stereology with Image J?

David Finkelstein wrote:

> Are there any Stereology plug ins for Image J.
> Specifically, an ability to drop\superimpose a counting frame (of user
> defined size and step size) onto a section image.  Then the ability to
zoom
> into each of the counting frames in order.

There's the "grid" plugin ("Draw line or point grids":
http://rsb.info.nih.gov/ij/plugins/grid.html).  It's good for randomly
creating a grid over an image, e.g. for cavalieri estimations of volume
or to create a random set of points for systematic random sampling.

For a counting frame, we simply draw one on a piece of acetate that we
tape to the computer monitor.  Very low-tech but it works.

The "IJStage and IJSerial (microscope stage control and serial I/O)"
plugin (http://www.eslide.net/ijstage.php) appears able to control some
types of stages but you'd need to program in the specifics for
systematic random sampling.

Good luck--

Martin Wessendorf

--
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: martinw[at]med.umn.edu

[Martin Wessendorf]

Jacqui Ross wrote:

> Since Martin has mentioned the Grid plugin which works well for
> systematic sampling, can anyone remind me how you designate the size of
> the grid relative to your image field that you should use for sampling
> for manual counting, etc.?

When you open the plugin, you get prompted to enter the values that you
want.  With regard to choosing the appropriate values--that'll depend
upon the variability in your system: the more variability within your
sections, the more grids you'd want to count per section.  The Howard
and Reed stereology book goes over this well; also there was a wonderful
little article by John Basgen in Microscopy Today that covered this,
sometime in the past two years.

Martin
--
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: martinw[at]med.umn.edu

[Jacqueline Ross]

Thanks very much Martin,

I'll have a look for the references you mentioned. I used to have a
rather good old stereology book when I was in Australia that was really
useful but unfortunately I didn't bring it back with me. I seem to
remember having to keep on sampling until the CV was below 5%...

Cheers,

Jacqui

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

Tel: [phone] Ext 87438
Fax: [phone]

http://www.health.auckland.ac.nz/biru/ 

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Martin Wessendorf
Sent: 05 January 2007 12:29
To: [hidden email]
Subject: Re: Stereology with Image J?

Jacqui Ross wrote:

> Since Martin has mentioned the Grid plugin which works well for
> systematic sampling, can anyone remind me how you designate the size
of
> the grid relative to your image field that you should use for sampling
> for manual counting, etc.?

When you open the plugin, you get prompted to enter the values that you
want.  With regard to choosing the appropriate values--that'll depend
upon the variability in your system: the more variability within your
sections, the more grids you'd want to count per section.  The Howard
and Reed stereology book goes over this well; also there was a wonderful

little article by John Basgen in Microscopy Today that covered this,
sometime in the past two years.

Martin
--
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: martinw[at]med.umn.edu

[dksamuel]

How much contrast will be there between the head and tail,Is it a stained
colored image (photo) or a live preview, anyway you have to define an area
as head is it circular and uniform sized, How many particles you plan to
measure, and what measurements, only length or perimeter or volume or all !,
please clarify, regards Samuel

On 1/4/07, Martin Wessendorf <[hidden email]> wrote:

>
> Somporn Duanyai wrote:
>
> > Please advise me how to use Image j for measuring sperm head area.
>
> What do you mean by the "sperm head area"?  The surface area?  Or the
> cross-sectional area?
>
> In either case, the answer that you obtain may depend as much on optical
> and stereological issues as it does on the specific method you use.
> Different species have different sized sperm heads; some are so small
> that it could be challenging to obtain an accurate measurement by
> optical microscopy.
>
> The stereological issues are outlined in CV Howard and MG Reed's book,
> "Unbiased Stereology".  If you haven't already, consult that or a
> similar book before you go too much further.
>
> Good luck!
>
> Martin Wessendorf
> --
> 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: martinw[at]med.umn.edu
>

[Gabriel Landini]

On Friday 05 January 2007 00:04, Jacqui Ross wrote:
> I'll have a look for the references you mentioned. I used to have a
> rather good old stereology book when I was in Australia that was really
> useful but unfortunately I didn't bring it back with me. I seem to
> remember having to keep on sampling until the CV was below 5%...

Not sure if it will help, but there is a link to Russ' stereology book
(published in pdf format somewhere in the web) at the Tudor site (in the
Links section).

G.

[Jacqueline Ross]

Thanks Gabriel,

I didn't know about that link so I'll check it out.

Cheers,

Jacqui.

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

Tel: [phone] Ext 87438
Fax: [phone]

http://www.health.auckland.ac.nz/biru/ 

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Gabriel Landini
Sent: 05 January 2007 22:28
To: [hidden email]
Subject: Re: Stereology with Image J?

On Friday 05 January 2007 00:04, Jacqui Ross wrote:
> I'll have a look for the references you mentioned. I used to have a
> rather good old stereology book when I was in Australia that was
really
> useful but unfortunately I didn't bring it back with me. I seem to
> remember having to keep on sampling until the CV was below 5%...

Not sure if it will help, but there is a link to Russ' stereology book
(published in pdf format somewhere in the web) at the Tudor site (in the

Links section).

G.