Lenght measurement

[Alexander V. Kalachev-2]

Dear ImageJ users,

for our current project we need to measure length of spermatozoa nucleus. It is curved in shape
(see example image attached, nucleus outlined with white dashed line) and we have no idea how to
measure its length. Could anyone provide us with an advice how to measure the length of such curved
figure?

With kind regards,
Alexander

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[Boris Golman]

Alexander:

If you like to measure the length of nucleus outline go to Analyze -> Set
measurements -> Perimeters and then Analyze --> Measure

If you like to have an average measure of nucleus length look for Feret's
diameter frequently used for measurement of particle diameters.

Anyway you need to have a definition of "length".

Uspexov.

Boris

On Mon, Jan 18, 2016 at 5:19 PM, Alexander V. Kalachev <
[hidden email]> wrote:

> Dear ImageJ users,
>
> for our current project we need to measure length of spermatozoa nucleus.
> It is curved in shape
> (see example image attached, nucleus outlined with white dashed line) and
> we have no idea how to
> measure its length. Could anyone provide us with an advice how to measure
> the length of such curved
> figure?
>
> With kind regards,
> Alexander
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Alexander V. Kalachev-2]

Dear Boris,

thank you for fast reply. Under the term "length" I meant the length of a line running from the
bottom to the top of nucleus and replicating nucleus' curvature (see attached image, black line).

Alexander

Mon, 18 Jan 2016 17:46:43 +0700
Boris Golman <[hidden email]>

> Alexander:
>
> If you like to measure the length of nucleus outline go to Analyze -> Set
> measurements -> Perimeters and then Analyze --> Measure
>
> If you like to have an average measure of nucleus length look for Feret's
> diameter frequently used for measurement of particle diameters.
>
> Anyway you need to have a definition of "length".
>
> Uspexov.
>
> Boris
>
> On Mon, Jan 18, 2016 at 5:19 PM, Alexander V. Kalachev <
> [hidden email]> wrote:
>
> > Dear ImageJ users,
> >
> > for our current project we need to measure length of spermatozoa nucleus.
> > It is curved in shape
> > (see example image attached, nucleus outlined with white dashed line) and
> > we have no idea how to
> > measure its length. Could anyone provide us with an advice how to measure
> > the length of such curved
> > figure?
> >
> > With kind regards,
> > Alexander
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Jan Eglinger]

Hi Alexander,

the "longest shortest path" option of the Analyze Skeleton plugin might
do what you need:
http://imagej.net/AnalyzeSkeleton

You might need to use some blurring of your nucleus before segmenting
and skeletonizing it, to avoid over-skeletonization.

Hope that helps,
Jan



On 18.01.2016 12:16, Alexander V. Kalachev wrote:

> Dear Boris,
>
> thank you for fast reply. Under the term "length" I meant the length of a line running from the
> bottom to the top of nucleus and replicating nucleus' curvature (see attached image, black line).
>
> Alexander
>
> Mon, 18 Jan 2016 17:46:43 +0700
> Boris Golman <[hidden email]>
>
>> Alexander:
>>
>> If you like to measure the length of nucleus outline go to Analyze -> Set
>> measurements -> Perimeters and then Analyze --> Measure
>>
>> If you like to have an average measure of nucleus length look for Feret's
>> diameter frequently used for measurement of particle diameters.
>>
>> Anyway you need to have a definition of "length".
>>
>> Uspexov.
>>
>> Boris
>>
>> On Mon, Jan 18, 2016 at 5:19 PM, Alexander V. Kalachev <
>> [hidden email]> wrote:
>>
>>> Dear ImageJ users,
>>>
>>> for our current project we need to measure length of spermatozoa nucleus.
>>> It is curved in shape
>>> (see example image attached, nucleus outlined with white dashed line) and
>>> we have no idea how to
>>> measure its length. Could anyone provide us with an advice how to measure
>>> the length of such curved
>>> figure?
>>>
>>> With kind regards,
>>> Alexander
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Leon Espinosa-3]

Maybe there is a different approach: as you have a kind of bend rectangle we can assume that Area = width x length . By thresholding/segmentation you can have a good measure of the area. And maybe you can manually measure 3 or 5 "widths" and calculate a mean width. Now a stimation of the length will be Area/meanWidth . With Feret or distance maps you can have an automatic and precise measure of the mean width.

All the best,

Leon


Le 18 janv. 2016 à 11:19, Alexander V. Kalachev a écrit :

> Dear ImageJ users,
>
> for our current project we need to measure length of spermatozoa nucleus. It is curved in shape
> (see example image attached, nucleus outlined with white dashed line) and we have no idea how to
> measure its length. Could anyone provide us with an advice how to measure the length of such curved
> figure?
>
> With kind regards,
> Alexander
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> <example.png>

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[Krs5]

Dear Alexander,

I could imagine something that creates a line between the start point, centre of mass and endpoint of your selection. Centre of mass can be found via Threshold, followed by Analyse Particles with Centre of mass selected in Set Measurements. After that use Edit > Selection > Fit Spline and measure the line.

Best wishes

Kees

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Leon Espinosa
Sent: 18 January 2016 12:51
To: [hidden email]
Subject: Re: Lenght measurement

Maybe there is a different approach: as you have a kind of bend rectangle we can assume that Area = width x length . By thresholding/segmentation you can have a good measure of the area. And maybe you can manually measure 3 or 5 "widths" and calculate a mean width. Now a stimation of the length will be Area/meanWidth . With Feret or distance maps you can have an automatic and precise measure of the mean width.

All the best,

Leon


Le 18 janv. 2016 à 11:19, Alexander V. Kalachev a écrit :

> Dear ImageJ users,
>
> for our current project we need to measure length of spermatozoa
> nucleus. It is curved in shape (see example image attached, nucleus
> outlined with white dashed line) and we have no idea how to measure
> its length. Could anyone provide us with an advice how to measure the length of such curved figure?
>
> With kind regards,
> Alexander
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> <example.png>

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[Kenneth Sloan-2]

This is a classic (and ancient) problem.  First - will you be automatically segmenting the nuclei?  If you are instead doing manual segmentation, the right answer is to have a trained observer draw the axis as well.

If you are automatically segmenting, then you need to also automatically estimate a so-called “medial axis”.  In the distant past, this was known as the “Blum Transform”, which was invented for precisely this problem.  It’s essentially what you get by skeletonizing.
The problem is that the medial axis is simple (and *almost* what you want), but in practice can be complicated by high frequency features of the segmented perimeter.  Someone has already mentioned blurring the image - I might suggest simplifying the perimeter.

I would probably try to bound the nuclei with a simplified polygon (putting a minimum length on each segment, and perhaps other constraints as well - motivated by knowledge of what a nucleus is “supposed to” look like).  But, that is far from an already built-in ImageJ function.

My best idea (assuming all nuclei look like the one shown) would be to fit a quadratic to the pixels in the nucleus.  Think of this as a cloud of data and find the best fitting quadratic to that cloud of points.  Then, find the points along that quadratic which intersect the boundary.  Finally, measure the length of that quadratic “line segment”.

You can do something similar with the skeleton - find the longest path subject to a constraint on the curvature, and then extend this (perhaps just extend the first and last segments) to the boundary.

Bottom line:  
 smooth the segmented nucleus,
 skeletonize,
 find a candidate piece of the skeleton that is long, without sharp turns
 extend this to the boundary on either end
 measure the length


--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.

> On Jan 18, 2016, at 04:19 , Alexander V. Kalachev <[hidden email]> wrote:
>
> Dear ImageJ users,
>
> for our current project we need to measure length of spermatozoa nucleus. It is curved in shape
> (see example image attached, nucleus outlined with white dashed line) and we have no idea how to
> measure its length. Could anyone provide us with an advice how to measure the length of such curved
> figure?
>
> With kind regards,
> Alexander
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> <example.png>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Robert Dougherty]

Alexander,

See Measure ROI Curve on http://www.optinav.com/Measure-Roi.htm

Bob

> On Jan 18, 2016, at 2:19 AM, Alexander V. Kalachev <[hidden email]> wrote:
>
> Dear ImageJ users,
>
> for our current project we need to measure length of spermatozoa nucleus. It is curved in shape
> (see example image attached, nucleus outlined with white dashed line) and we have no idea how to
> measure its length. Could anyone provide us with an advice how to measure the length of such curved
> figure?
>
> With kind regards,
> Alexander
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> <example.png>

Robert P. Dougherty
President
OptiNav, Inc.
1414 127th Pl NE #106
Bellevue, WA 98005
[phone]
FAX [phone]
[hidden email]
www.optinav. com

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[Jacqueline Ross]

Hi Alexander,

Could you please post an image without any graphics/lines on it? It might be quite straightforward to try segmentation followed by skeletonization as Jan has suggested or someone may come up with another method that will work automatically but we can't really test out options with the image you sent:-).

Cheers,

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 1142, NEW ZEALAND

Tel: [phone]
Fax: [phone]

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


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Alexander V. Kalachev
Sent: Tuesday, 19 January 2016 12:17 a.m.
To: [hidden email]
Subject: Re: Lenght measurement

Dear Boris,

thank you for fast reply. Under the term "length" I meant the length of a line running from the bottom to the top of nucleus and replicating nucleus' curvature (see attached image, black line).

Alexander

Mon, 18 Jan 2016 17:46:43 +0700
Boris Golman <[hidden email]>

> Alexander:
>
> If you like to measure the length of nucleus outline go to Analyze ->
> Set measurements -> Perimeters and then Analyze --> Measure
>
> If you like to have an average measure of nucleus length look for
> Feret's diameter frequently used for measurement of particle diameters.
>
> Anyway you need to have a definition of "length".
>
> Uspexov.
>
> Boris
>
> On Mon, Jan 18, 2016 at 5:19 PM, Alexander V. Kalachev <
> [hidden email]> wrote:
>
> > Dear ImageJ users,
> >
> > for our current project we need to measure length of spermatozoa nucleus.
> > It is curved in shape
> > (see example image attached, nucleus outlined with white dashed
> > line) and we have no idea how to measure its length. Could anyone
> > provide us with an advice how to measure the length of such curved
> > figure?
> >
> > With kind regards,
> > Alexander
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Alexander V. Kalachev-2]

Dear all,

thank you for your replies. We have found a lot of information for our work. I've asked colleague
of mine for image without any graphics. As soon as she will provide me with such an image I will
send it to you. At the moment we've managed to measure Feret's diameter. But path measurements on
skeletonized images seems to be very interesting option. thank you for your replies. We have found
a lot of information for our work. I've asked colleague of mine for image without any graphics. As
soon as she will provide me with such an image I will send it to you. At the moment we've managed
to measure Feret's diameter.

With kind regards,
Alexander

Mon, 18 Jan 2016 23:45:16 +0000
Jacqui Ross <[hidden email]>

> Hi Alexander,
>
> Could you please post an image without any graphics/lines on it? It might be quite straightforward to try segmentation followed by skeletonization as Jan has suggested or someone may come up with another method that will work automatically but we can't really test out options with the image you sent:-).
>
> Cheers,
>
> 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 1142, NEW ZEALAND
>
> Tel: [phone]
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Alexander V. Kalachev
> Sent: Tuesday, 19 January 2016 12:17 a.m.
> To: [hidden email]
> Subject: Re: Lenght measurement
>
> Dear Boris,
>
> thank you for fast reply. Under the term "length" I meant the length of a line running from the bottom to the top of nucleus and replicating nucleus' curvature (see attached image, black line).
>
> Alexander
>
> Mon, 18 Jan 2016 17:46:43 +0700
> Boris Golman <[hidden email]>
>
> > Alexander:
> >
> > If you like to measure the length of nucleus outline go to Analyze ->
> > Set measurements -> Perimeters and then Analyze --> Measure
> >
> > If you like to have an average measure of nucleus length look for
> > Feret's diameter frequently used for measurement of particle diameters.
> >
> > Anyway you need to have a definition of "length".
> >
> > Uspexov.
> >
> > Boris
> >
> > On Mon, Jan 18, 2016 at 5:19 PM, Alexander V. Kalachev <
> > [hidden email]> wrote:
> >
> > > Dear ImageJ users,
> > >
> > > for our current project we need to measure length of spermatozoa nucleus.
> > > It is curved in shape
> > > (see example image attached, nucleus outlined with white dashed
> > > line) and we have no idea how to measure its length. Could anyone
> > > provide us with an advice how to measure the length of such curved
> > > figure?
> > >
> > > With kind regards,
> > > Alexander
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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