curvature along the outline of a thresholded object

[foxtango]

Hi everybody,

is anybody aware of a plugin that calculates the curvature along the
outline of a thresholded object?

thank you, Thomas

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[Robert Dougherty]

Thomas,Measure ROI on OptiNav.info exists, but I have not touched it in more than a decade....Bob


Sent from Smallbiz Yahoo Mail for iPhone


On Monday, June 29, 2020, 1:06 PM, Thomas Fischer <[hidden email]> wrote:

Hi everybody,

is anybody aware of a plugin that calculates the curvature along the
outline of a thresholded object?

thank you, Thomas

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




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

[foxtango]

Thank you Bob,

I looked at the description and could not find what I am aiming for.

If after thresholding the object is perfectly circular, the result should
be a constant value versus the pixels along the outline. If the object is
bumpy, the function would not be constant any more. If part of the outline
is concave the function would be negative there.

Are you sure the plugin you mentioned does that?

Best, Thomas

Am Mo., 29. Juni 2020 um 22:40 Uhr schrieb Robert Dougherty <[hidden email]
>:

> Thomas,Measure ROI on OptiNav.info exists, but I have not touched it in
> more than a decade....Bob
>
>
> Sent from Smallbiz Yahoo Mail for iPhone
>
>
> On Monday, June 29, 2020, 1:06 PM, Thomas Fischer <[hidden email]>
> wrote:
>
> Hi everybody,
>
> is anybody aware of a plugin that calculates the curvature along the
> outline of a thresholded object?
>
> thank you, Thomas
>
> --
> 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

[Robert Dougherty]

 Thomas,
The plugin measures arc length.  I read your question too fast.  Measuring curvature sounds interesting and I think the plugin could be modified to do it, but I don't know if that is the easiest way to a solution.
Bob

    On Monday, June 29, 2020, 2:26:25 PM PDT, Thomas Fischer <[hidden email]> wrote:  
 
 Thank you Bob,

I looked at the description and could not find what I am aiming for.

If after thresholding the object is perfectly circular, the result should
be a constant value versus the pixels along the outline. If the object is
bumpy, the function would not be constant any more. If part of the outline
is concave the function would be negative there.

Are you sure the plugin you mentioned does that?

Best, Thomas

Am Mo., 29. Juni 2020 um 22:40 Uhr schrieb Robert Dougherty <[hidden email]
>:

> Thomas,Measure ROI on OptiNav.info exists, but I have not touched it in
> more than a decade....Bob
>
>
> Sent from Smallbiz Yahoo Mail for iPhone
>
>
> On Monday, June 29, 2020, 1:06 PM, Thomas Fischer <[hidden email]>
> wrote:
>
> Hi everybody,
>
> is anybody aware of a plugin that calculates the curvature along the
> outline of a thresholded object?
>
> thank you, Thomas
>
> --
> 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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[Herbie]

Good day Thomas,

it would be interesting to know what you are going to do with the result
of such curvature shape description.

If it is e.g. for invariant shape descriptions, I recommend having a
look at Fourier-shape descriptors. There exist at least two
ImageJ-plugins for this purpose.

Regards

Herbie

::::::::::::::::::::::::::::::::::::::::::::
Am 29.06.20 um 23:24 schrieb Thomas Fischer:

> Thank you Bob,
>
> I looked at the description and could not find what I am aiming for.
>
> If after thresholding the object is perfectly circular, the result should
> be a constant value versus the pixels along the outline. If the object is
> bumpy, the function would not be constant any more. If part of the outline
> is concave the function would be negative there.
>
> Are you sure the plugin you mentioned does that?
>
> Best, Thomas
>
> Am Mo., 29. Juni 2020 um 22:40 Uhr schrieb Robert Dougherty <[hidden email]
>> :
>
>> Thomas,Measure ROI on OptiNav.info exists, but I have not touched it in
>> more than a decade....Bob
>>
>>
>> Sent from Smallbiz Yahoo Mail for iPhone
>>
>>
>> On Monday, June 29, 2020, 1:06 PM, Thomas Fischer <[hidden email]>
>> wrote:
>>
>> Hi everybody,
>>
>> is anybody aware of a plugin that calculates the curvature along the
>> outline of a thresholded object?
>>
>> thank you, Thomas
>>
>> --
>> 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

[Thomas Boudier-5]

Hi Thomas,

As mentioned by Herbie, you can have a look to the Fourier Shape
Analysis, a very old plugin too ;-) .

https://imagejdocu.list.lu/plugin/analysis/fourier_shape_analysis/start

Best,

Thomas

On 6/30/20 5:24 AM, Thomas Fischer wrote:

> Thank you Bob,
>
> I looked at the description and could not find what I am aiming for.
>
> If after thresholding the object is perfectly circular, the result should
> be a constant value versus the pixels along the outline. If the object is
> bumpy, the function would not be constant any more. If part of the outline
> is concave the function would be negative there.
>
> Are you sure the plugin you mentioned does that?
>
> Best, Thomas
>
> Am Mo., 29. Juni 2020 um 22:40 Uhr schrieb Robert Dougherty
> <[hidden email]
>> :
>> Thomas,Measure ROI on OptiNav.info exists, but I have not touched it in
>> more than a decade....Bob
>>
>>
>> Sent from Smallbiz Yahoo Mail for iPhone
>>
>>
>> On Monday, June 29, 2020, 1:06 PM, Thomas Fischer <[hidden email]>
>> wrote:
>>
>> Hi everybody,
>>
>> is anybody aware of a plugin that calculates the curvature along the
>> outline of a thresholded object?
>>
>> thank you, Thomas
>>
>> --
>> 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

--
Thomas Boudier, Assoc. Prof. Scholar,
Institute Molecular Biology,
Academia Sinica, Taipei, Taiwan

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

[foxtango]

Hi Thomas and Herbie,
I want to distinguish shapes with partly convex contours (0453.tif) or
bumpy contours (0087.tif) from shapes without such distortions (0002.tif).
The fourier shape analysis plugin obviously requires a selection that
follows the contour. I suspect that to this end the Shape_Smoothing_.jar
is used. But it requires additional software. On page
https://github.com/wendykierp/JTransforms three different downloads are
possible. Do I need all of them? As to ijblob, I don't know what to do on
page https://github.com/thorstenwagner/ij-blob
Regards, Thomas

Am Di., 30. Juni 2020 um 10:31 Uhr schrieb Thomas Boudier <
[hidden email]>:

> Hi Thomas,
>
> As mentioned by Herbie, you can have a look to the Fourier Shape
> Analysis, a very old plugin too ;-) .
>
> https://imagejdocu.list.lu/plugin/analysis/fourier_shape_analysis/start
>
> Best,
>
> Thomas
>
> On 6/30/20 5:24 AM, Thomas Fischer wrote:
> > Thank you Bob,
> >
> > I looked at the description and could not find what I am aiming for.
> >
> > If after thresholding the object is perfectly circular, the result should
> > be a constant value versus the pixels along the outline. If the object is
> > bumpy, the function would not be constant any more. If part of the
> outline
> > is concave the function would be negative there.
> >
> > Are you sure the plugin you mentioned does that?
> >
> > Best, Thomas
> >
> > Am Mo., 29. Juni 2020 um 22:40 Uhr schrieb Robert Dougherty
> > <[hidden email]
> >> :
> >> Thomas,Measure ROI on OptiNav.info exists, but I have not touched it in
> >> more than a decade....Bob
> >>
> >>
> >> Sent from Smallbiz Yahoo Mail for iPhone
> >>
> >>
> >> On Monday, June 29, 2020, 1:06 PM, Thomas Fischer <[hidden email]
> >
> >> wrote:
> >>
> >> Hi everybody,
> >>
> >> is anybody aware of a plugin that calculates the curvature along the
> >> outline of a thresholded object?
> >>
> >> thank you, Thomas
> >>
> >> --
> >> 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
>
> --
> Thomas Boudier, Assoc. Prof. Scholar,
> Institute Molecular Biology,
> Academia Sinica, Taipei, Taiwan
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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[Herbie]

"The fourier shape analysis plugin obviously requires a selection that
follows the contour."

I fear that this holds as well if you are looking for local curvatures.
Is there any problem with getting the selection of binary objects?

In any case, you will be able to distinguish the shapes using
Fourier-descriptors.

A good treatment of Fourier-descriptors with Java-code is given in:
Wilhelm Burger and Mark J. Burge (2016)
"Digital Image Processing: An Algorithmic Introduction Using Java"
Springer

Regards

Herbie

::::::::::::::::::::::::::::::::::::::::::::
Am 30.06.20 um 13:57 schrieb Thomas Fischer:

> Hi Thomas and Herbie,
> I want to distinguish shapes with partly convex contours (0453.tif) or
> bumpy contours (0087.tif) from shapes without such distortions (0002.tif).
> The fourier shape analysis plugin obviously requires a selection that
> follows the contour. I suspect that to this end the Shape_Smoothing_.jar
> is used. But it requires additional software. On page
> https://github.com/wendykierp/JTransforms three different downloads are
> possible. Do I need all of them? As to ijblob, I don't know what to do on
> page https://github.com/thorstenwagner/ij-blob
> Regards, Thomas
>
> Am Di., 30. Juni 2020 um 10:31 Uhr schrieb Thomas Boudier <
> [hidden email]>:
>
>> Hi Thomas,
>>
>> As mentioned by Herbie, you can have a look to the Fourier Shape
>> Analysis, a very old plugin too ;-) .
>>
>> https://imagejdocu.list.lu/plugin/analysis/fourier_shape_analysis/start
>>
>> Best,
>>
>> Thomas
>>
>> On 6/30/20 5:24 AM, Thomas Fischer wrote:
>>> Thank you Bob,
>>>
>>> I looked at the description and could not find what I am aiming for.
>>>
>>> If after thresholding the object is perfectly circular, the result should
>>> be a constant value versus the pixels along the outline. If the object is
>>> bumpy, the function would not be constant any more. If part of the
>> outline
>>> is concave the function would be negative there.
>>>
>>> Are you sure the plugin you mentioned does that?
>>>
>>> Best, Thomas
>>>
>>> Am Mo., 29. Juni 2020 um 22:40 Uhr schrieb Robert Dougherty
>>> <[hidden email]
>>>> :
>>>> Thomas,Measure ROI on OptiNav.info exists, but I have not touched it in
>>>> more than a decade....Bob
>>>>
>>>>
>>>> Sent from Smallbiz Yahoo Mail for iPhone
>>>>
>>>>
>>>> On Monday, June 29, 2020, 1:06 PM, Thomas Fischer <[hidden email]
>>>
>>>> wrote:
>>>>
>>>> Hi everybody,
>>>>
>>>> is anybody aware of a plugin that calculates the curvature along the
>>>> outline of a thresholded object?
>>>>
>>>> thank you, Thomas
>>>>
>>>> --
>>>> 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
>>
>> --
>> Thomas Boudier, Assoc. Prof. Scholar,
>> Institute Molecular Biology,
>> Academia Sinica, Taipei, Taiwan
>>
>> --
>> 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

[Michael Schmid]

Hi Thomas,

you can convert your mask to a selection with Edit>Selection>Create
Selection or with the Wand Tool (the latter is needed if you have more
than one object).
If you want, you can then use Edit>Selection>Fit Spline.

These commands are in the core of ImageJ and require no extra download.

Michael
________________________________________________________________
On 30.06.20 13:57, Thomas Fischer wrote:

> Hi Thomas and Herbie,
> I want to distinguish shapes with partly convex contours (0453.tif) or
> bumpy contours (0087.tif) from shapes without such distortions (0002.tif).
> The fourier shape analysis plugin obviously requires a selection that
> follows the contour. I suspect that to this end the Shape_Smoothing_.jar
> is used. But it requires additional software. On page
> https://github.com/wendykierp/JTransforms three different downloads are
> possible. Do I need all of them? As to ijblob, I don't know what to do on
> page https://github.com/thorstenwagner/ij-blob
> Regards, Thomas
>
> Am Di., 30. Juni 2020 um 10:31 Uhr schrieb Thomas Boudier <
> [hidden email]>:
>
>> Hi Thomas,
>>
>> As mentioned by Herbie, you can have a look to the Fourier Shape
>> Analysis, a very old plugin too ;-) .
>>
>> https://imagejdocu.list.lu/plugin/analysis/fourier_shape_analysis/start
>>
>> Best,
>>
>> Thomas
>>
>> On 6/30/20 5:24 AM, Thomas Fischer wrote:
>>> Thank you Bob,
>>>
>>> I looked at the description and could not find what I am aiming for.
>>>
>>> If after thresholding the object is perfectly circular, the result should
>>> be a constant value versus the pixels along the outline. If the object is
>>> bumpy, the function would not be constant any more. If part of the
>> outline
>>> is concave the function would be negative there.
>>>
>>> Are you sure the plugin you mentioned does that?
>>>
>>> Best, Thomas
>>>
>>> Am Mo., 29. Juni 2020 um 22:40 Uhr schrieb Robert Dougherty
>>> <[hidden email]
>>>> :
>>>> Thomas,Measure ROI on OptiNav.info exists, but I have not touched it in
>>>> more than a decade....Bob
>>>>
>>>>
>>>> Sent from Smallbiz Yahoo Mail for iPhone
>>>>
>>>>
>>>> On Monday, June 29, 2020, 1:06 PM, Thomas Fischer <[hidden email]
>>>
>>>> wrote:
>>>>
>>>> Hi everybody,
>>>>
>>>> is anybody aware of a plugin that calculates the curvature along the
>>>> outline of a thresholded object?
>>>>
>>>> thank you, Thomas
>>>>
>>>> --
>>>> 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
>>
>> --
>> Thomas Boudier, Assoc. Prof. Scholar,
>> Institute Molecular Biology,
>> Academia Sinica, Taipei, Taiwan
>>
>> --
>> 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

[foxtango]

Thank you Bob Herbie Thomas Michael,

after playing with the parameters, I can use the plugin. For curiosity a
question to Thomas. The curvature values are independent, whether the box
use calibration is checked or not. I assume it refers to a value that is
set outside the plugin.

best, regards, thomas

Am Di., 30. Juni 2020 um 17:14 Uhr schrieb Michael Schmid <
[hidden email]>:

> Hi Thomas,
>
> you can convert your mask to a selection with Edit>Selection>Create
> Selection or with the Wand Tool (the latter is needed if you have more
> than one object).
> If you want, you can then use Edit>Selection>Fit Spline.
>
> These commands are in the core of ImageJ and require no extra download.
>
> Michael
> ________________________________________________________________
> On 30.06.20 13:57, Thomas Fischer wrote:
> > Hi Thomas and Herbie,
> > I want to distinguish shapes with partly convex contours (0453.tif) or
> > bumpy contours (0087.tif) from shapes without such distortions
> (0002.tif).
> > The fourier shape analysis plugin obviously requires a selection that
> > follows the contour. I suspect that to this end the Shape_Smoothing_.jar
> > is used. But it requires additional software. On page
> > https://github.com/wendykierp/JTransforms three different downloads are
> > possible. Do I need all of them? As to ijblob, I don't know what to do on
> > page https://github.com/thorstenwagner/ij-blob
> > Regards, Thomas
> >
> > Am Di., 30. Juni 2020 um 10:31 Uhr schrieb Thomas Boudier <
> > [hidden email]>:
> >
> >> Hi Thomas,
> >>
> >> As mentioned by Herbie, you can have a look to the Fourier Shape
> >> Analysis, a very old plugin too ;-) .
> >>
> >> https://imagejdocu.list.lu/plugin/analysis/fourier_shape_analysis/start
> >>
> >> Best,
> >>
> >> Thomas
> >>
> >> On 6/30/20 5:24 AM, Thomas Fischer wrote:
> >>> Thank you Bob,
> >>>
> >>> I looked at the description and could not find what I am aiming for.
> >>>
> >>> If after thresholding the object is perfectly circular, the result
> should
> >>> be a constant value versus the pixels along the outline. If the object
> is
> >>> bumpy, the function would not be constant any more. If part of the
> >> outline
> >>> is concave the function would be negative there.
> >>>
> >>> Are you sure the plugin you mentioned does that?
> >>>
> >>> Best, Thomas
> >>>
> >>> Am Mo., 29. Juni 2020 um 22:40 Uhr schrieb Robert Dougherty
> >>> <[hidden email]
> >>>> :
> >>>> Thomas,Measure ROI on OptiNav.info exists, but I have not touched it
> in
> >>>> more than a decade....Bob
> >>>>
> >>>>
> >>>> Sent from Smallbiz Yahoo Mail for iPhone
> >>>>
> >>>>
> >>>> On Monday, June 29, 2020, 1:06 PM, Thomas Fischer <
> [hidden email]
> >>>
> >>>> wrote:
> >>>>
> >>>> Hi everybody,
> >>>>
> >>>> is anybody aware of a plugin that calculates the curvature along the
> >>>> outline of a thresholded object?
> >>>>
> >>>> thank you, Thomas
> >>>>
> >>>> --
> >>>> 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
> >>
> >> --
> >> Thomas Boudier, Assoc. Prof. Scholar,
> >> Institute Molecular Biology,
> >> Academia Sinica, Taipei, Taiwan
> >>
> >> --
> >> 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

[Thomas Boudier-5]

Hi Thomas,

If the image is calibrated, the curvature values will be computed
according to the pixel calibration.

Best,

Thomas

On 7/1/20 9:04 PM, Thomas Fischer wrote:

> Thank you Bob Herbie Thomas Michael,
>
> after playing with the parameters, I can use the plugin. For curiosity a
> question to Thomas. The curvature values are independent, whether the box
> use calibration is checked or not. I assume it refers to a value that is
> set outside the plugin.
>
> best, regards, thomas
>
> Am Di., 30. Juni 2020 um 17:14 Uhr schrieb Michael Schmid <
> [hidden email]>:
>
>> Hi Thomas,
>>
>> you can convert your mask to a selection with Edit>Selection>Create
>> Selection or with the Wand Tool (the latter is needed if you have more
>> than one object).
>> If you want, you can then use Edit>Selection>Fit Spline.
>>
>> These commands are in the core of ImageJ and require no extra download.
>>
>> Michael
>> ________________________________________________________________
>> On 30.06.20 13:57, Thomas Fischer wrote:
>>> Hi Thomas and Herbie,
>>> I want to distinguish shapes with partly convex contours (0453.tif) or
>>> bumpy contours (0087.tif) from shapes without such distortions
>> (0002.tif).
>>> The fourier shape analysis plugin obviously requires a selection that
>>> follows the contour. I suspect that to this end the Shape_Smoothing_.jar
>>> is used. But it requires additional software. On page
>>> https://github.com/wendykierp/JTransforms three different downloads are
>>> possible. Do I need all of them? As to ijblob, I don't know what to do on
>>> page https://github.com/thorstenwagner/ij-blob
>>> Regards, Thomas
>>>
>>> Am Di., 30. Juni 2020 um 10:31 Uhr schrieb Thomas Boudier <
>>> [hidden email]>:
>>>
>>>> Hi Thomas,
>>>>
>>>> As mentioned by Herbie, you can have a look to the Fourier Shape
>>>> Analysis, a very old plugin too ;-) .
>>>>
>>>> https://imagejdocu.list.lu/plugin/analysis/fourier_shape_analysis/start
>>>>
>>>> Best,
>>>>
>>>> Thomas
>>>>
>>>> On 6/30/20 5:24 AM, Thomas Fischer wrote:
>>>>> Thank you Bob,
>>>>>
>>>>> I looked at the description and could not find what I am aiming for.
>>>>>
>>>>> If after thresholding the object is perfectly circular, the result
>> should
>>>>> be a constant value versus the pixels along the outline. If the object
>> is
>>>>> bumpy, the function would not be constant any more. If part of the
>>>> outline
>>>>> is concave the function would be negative there.
>>>>>
>>>>> Are you sure the plugin you mentioned does that?
>>>>>
>>>>> Best, Thomas
>>>>>
>>>>> Am Mo., 29. Juni 2020 um 22:40 Uhr schrieb Robert Dougherty
>>>>> <[hidden email]
>>>>>> :
>>>>>> Thomas,Measure ROI on OptiNav.info exists, but I have not touched it
>> in
>>>>>> more than a decade....Bob
>>>>>>
>>>>>>
>>>>>> Sent from Smallbiz Yahoo Mail for iPhone
>>>>>>
>>>>>>
>>>>>> On Monday, June 29, 2020, 1:06 PM, Thomas Fischer <
>> [hidden email]
>>>>>> wrote:
>>>>>>
>>>>>> Hi everybody,
>>>>>>
>>>>>> is anybody aware of a plugin that calculates the curvature along the
>>>>>> outline of a thresholded object?
>>>>>>
>>>>>> thank you, Thomas
>>>>>>
>>>>>> --
>>>>>> 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
>>>> --
>>>> Thomas Boudier, Assoc. Prof. Scholar,
>>>> Institute Molecular Biology,
>>>> Academia Sinica, Taipei, Taiwan
>>>>
>>>> --
>>>> 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

--
Thomas Boudier, Assoc. Prof. Scholar,
Institute Molecular Biology,
Academia Sinica, Taipei, Taiwan

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

[Robert Dougherty]

 Thomas,
I put a curvature plugin at http://www.optinav.info/Curvature.htm  It might be easier to use than the spline. I know it is for me, since I don't see how to use the spine to get curvature at all....

Bob

    On Monday, June 29, 2020, 2:26:25 PM PDT, Thomas Fischer <[hidden email]> wrote:  
 
 Thank you Bob,

I looked at the description and could not find what I am aiming for.

If after thresholding the object is perfectly circular, the result should
be a constant value versus the pixels along the outline. If the object is
bumpy, the function would not be constant any more. If part of the outline
is concave the function would be negative there.

Are you sure the plugin you mentioned does that?

Best, Thomas

Am Mo., 29. Juni 2020 um 22:40 Uhr schrieb Robert Dougherty <[hidden email]
>:

> Thomas,Measure ROI on OptiNav.info exists, but I have not touched it in
> more than a decade....Bob
>
>
> Sent from Smallbiz Yahoo Mail for iPhone
>
>
> On Monday, June 29, 2020, 1:06 PM, Thomas Fischer <[hidden email]>
> wrote:
>
> Hi everybody,
>
> is anybody aware of a plugin that calculates the curvature along the
> outline of a thresholded object?
>
> thank you, Thomas
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Gabriel Landini]

On Saturday, 4 July 2020 02:58:14 BST you wrote:
> I put a curvature plugin at http://www.optinav.info/Curvature.htm  It might
> be easier to use than the spline. I know it is for me, since I don't see
> how to use the spine to get curvature at all....

Hi Bob, I tried this, but if gives an error that says:
Unrecognized command: "Phase".

When attempting to compile the source code it says:
<<Plugins that call IJ.run() should probably implement PlugIn, not
PlugInFilter.>>

I am running IJ 1.53d8 and tried Java 1.6 and 1.8 under linux.
Regards

Gabriel

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[Herbie]

Dear Gabriel,

Bob's plugin runs fine here on a Mac with ImageJ 1.53c and Java 1.8.0_251.

Result appended.

The additional colour-coding of the resulting float-image is surprising.

Kind regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::
Am 04.07.20 um 16:20 schrieb Gabriel Landini:

> On Saturday, 4 July 2020 02:58:14 BST you wrote:
>> I put a curvature plugin at http://www.optinav.info/Curvature.htm  It might
>> be easier to use than the spline. I know it is for me, since I don't see
>> how to use the spine to get curvature at all....
>
> Hi Bob, I tried this, but if gives an error that says:
> Unrecognized command: "Phase".
>
> When attempting to compile the source code it says:
> <<Plugins that call IJ.run() should probably implement PlugIn, not
> PlugInFilter.>>
>
> I am running IJ 1.53d8 and tried Java 1.6 and 1.8 under linux.
> Regards
>
> Gabriel
>
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[Gabriel Landini]

Thanks to Herbie, I now know that this was a case of me having previously
renamed the Phase.lut (!)
The plugin works fine.

Regards
Gabriel

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[Robert Dougherty]

 Gabriel,
In the meantime, I tried and failed to track down how ImageJ is supposed to load the Phase LUT. Giving up, I changed the code to use another sign-friendly LUT that I coded explicitly.  Now Curvature displays the results in green-blue. Going forward, it may be a question of which color scheme is better.  One could experiment by running the new version of Curvature and then manually changing the LUT to Phase to simulate the old version.  Perhaps green-blue is better for colorblindness than the red-blue scheme of Phase?

Bob

    On Saturday, July 4, 2020, 9:47:55 AM PDT, Gabriel Landini <[hidden email]> wrote:  
 
 Thanks to Herbie, I now know that this was a case of me having previously
renamed the Phase.lut (!)
The plugin works fine.

Regards
Gabriel

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[Gabriel Landini]

Thanks Bob, I can confirm that it works fine.
I think colourblind observers (red-green type) would see the green as some
shades of yellow and blue as blue. At lease that is what the Dichromacy plugin
shows.
Regards

Gabriel


On Saturday, 4 July 2020 18:05:09 BST you wrote:

>  Gabriel,
> In the meantime, I tried and failed to track down how ImageJ is supposed to
> load the Phase LUT. Giving up, I changed the code to use another
> sign-friendly LUT that I coded explicitly.  Now Curvature displays the
> results in green-blue. Going forward, it may be a question of which color
> scheme is better.  One could experiment by running the new version of
> Curvature and then manually changing the LUT to Phase to simulate the old
> version.  Perhaps green-blue is better for colorblindness than the red-blue
> scheme of Phase?
>
> Bob

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[Robert Dougherty]

 Gabriel,
Thanks.  In case it matters, there is a new version with smoother calculation and a black background.
Bob

    On Saturday, July 4, 2020, 11:33:56 AM PDT, Gabriel Landini <[hidden email]> wrote:  
 
 Thanks Bob, I can confirm that it works fine.
I think colourblind observers (red-green type) would see the green as some
shades of yellow and blue as blue. At lease that is what the Dichromacy plugin
shows.
Regards

Gabriel


On Saturday, 4 July 2020 18:05:09 BST you wrote:

>  Gabriel,
> In the meantime, I tried and failed to track down how ImageJ is supposed to
> load the Phase LUT. Giving up, I changed the code to use another
> sign-friendly LUT that I coded explicitly.  Now Curvature displays the
> results in green-blue. Going forward, it may be a question of which color
> scheme is better.  One could experiment by running the new version of
> Curvature and then manually changing the LUT to Phase to simulate the old
> version.  Perhaps green-blue is better for colorblindness than the red-blue
> scheme of Phase?
>
> Bob

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[foxtango]

Dear Bob,

My reply is late because I had computer problems. The result of the plugin
looks nice. In order to use it I would need two features
1) A parameter to tune the sensitivity. Right now it is not sensitive
enough for my purpose. I am aware that an increase in sensitivity would
make the result more noisy. But as with the plugin of Thomas I would do the
smoothing afterwards.
2) A list of the curvature values along the circumference. Just looking at
the nice result is not enough in my case. I have to extract numbers from
this list.

I am content with the plugin of Thomas. But as we say in German: the better
is the enemy of the good.

Best regards, Thomas





Am So., 5. Juli 2020 um 07:33 Uhr schrieb Robert Dougherty <[hidden email]
>:

>  Gabriel,
> Thanks.  In case it matters, there is a new version with smoother
> calculation and a black background.
> Bob
>
>     On Saturday, July 4, 2020, 11:33:56 AM PDT, Gabriel Landini <
> [hidden email]> wrote:
>
>  Thanks Bob, I can confirm that it works fine.
> I think colourblind observers (red-green type) would see the green as some
> shades of yellow and blue as blue. At lease that is what the Dichromacy
> plugin
> shows.
> Regards
>
> Gabriel
>
>
> On Saturday, 4 July 2020 18:05:09 BST you wrote:
> >  Gabriel,
> > In the meantime, I tried and failed to track down how ImageJ is supposed
> to
> > load the Phase LUT. Giving up, I changed the code to use another
> > sign-friendly LUT that I coded explicitly.  Now Curvature displays the
> > results in green-blue. Going forward, it may be a question of which color
> > scheme is better.  One could experiment by running the new version of
> > Curvature and then manually changing the LUT to Phase to simulate the old
> > version.  Perhaps green-blue is better for colorblindness than the
> red-blue
> > scheme of Phase?
> >
> > Bob
>
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>
>
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>

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[Robert Dougherty]

Thomas,Thanks for the feedback and context.  There are several things I want to do with this, but I need to focus on my day job for a while.Bob


Sent from Smallbiz Yahoo Mail for iPhone


On Sunday, July 5, 2020, 10:14 AM, Thomas Fischer <[hidden email]> wrote:

Dear Bob,

My reply is late because I had computer problems. The result of the plugin
looks nice. In order to use it I would need two features
1) A parameter to tune the sensitivity. Right now it is not sensitive
enough for my purpose. I am aware that an increase in sensitivity would
make the result more noisy. But as with the plugin of Thomas I would do the
smoothing afterwards.
2) A list of the curvature values along the circumference. Just looking at
the nice result is not enough in my case. I have to extract numbers from
this list.

I am content with the plugin of Thomas. But as we say in German: the better
is the enemy of the good.

Best regards, Thomas





Am So., 5. Juli 2020 um 07:33 Uhr schrieb Robert Dougherty <[hidden email]
>:

>  Gabriel,
> Thanks.  In case it matters, there is a new version with smoother
> calculation and a black background.
> Bob
>
>    On Saturday, July 4, 2020, 11:33:56 AM PDT, Gabriel Landini <
> [hidden email]> wrote:
>
>  Thanks Bob, I can confirm that it works fine.
> I think colourblind observers (red-green type) would see the green as some
> shades of yellow and blue as blue. At lease that is what the Dichromacy
> plugin
> shows.
> Regards
>
> Gabriel
>
>
> On Saturday, 4 July 2020 18:05:09 BST you wrote:
> >  Gabriel,
> > In the meantime, I tried and failed to track down how ImageJ is supposed
> to
> > load the Phase LUT. Giving up, I changed the code to use another
> > sign-friendly LUT that I coded explicitly.  Now Curvature displays the
> > results in green-blue. Going forward, it may be a question of which color
> > scheme is better.  One could experiment by running the new version of
> > Curvature and then manually changing the LUT to Phase to simulate the old
> > version.  Perhaps green-blue is better for colorblindness than the
> red-blue
> > scheme of Phase?
> >
> > Bob
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
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>

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