Re: Quantification of axon Twist

Posted by Eric Denarier on Mar 24, 2017; 4:55pm
URL: http://imagej.273.s1.nabble.com/Quantification-of-axon-Twist-tp5018355p5018370.html

Thanks Straub and Herbie,


Thanks for your suggestions. I will try to figure out how to handle the
porblem.

At the end I want to get a measure of the change in orientation and be
able to compare several images coming from different genotype.

As I have been suggested I may have to cut the images into sector and
get a value of the major axis of orientation in each sector and its
coherency.


Eric Denarier
Grenoble Institut des Neurosciences
Inserm U1216
Chemin Fortuné Ferrini
38700 La Tronche
France

Tél :[phone]

http://neurosciences.ujf-grenoble.fr/

Le 24/03/2017 à 14:34, Straub, Volko A. (Dr.) a écrit :

> I noticed previously a 'Directionality' plugin in ImageJ that may be of use (https://imagej.net/Directionality). I only looked at it briefly a while ago and don't have any real experience with it, but it looks like it might be useful for your purpose.
>
> Volko
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Herbie
> Sent: 23 March 2017 19:00
> To: [hidden email]
> Subject: Re: Quantification of axon Twist
>
> Dear Eric,
>
> thanks for your explanation concerning the source of your image. So the neurons are grown on glass...
>
> re: Orientation Salience Function
>
> Here are links for two papers dealing with theoretical and algorithmic aspects. If you don't have much time, please try to understand at least the first two pages of the report (2013).
>
> <http://www.gluender.de/Writings/WritingsTexts/WritingsDownloads/1986_IntegralsCentralSlices.zip>
> <http://www.gluender.de/Writings/WritingsTexts/WritingsDownloads/2013_Orientation.zip>
>
> In fact Orientation Salience Functions are weighted histograms and could be normalized as such. Weighted, because they don' reflect the pure geometric property of orientation but the contrast/brightness of the image structures as well.
>
> With your image, it is interesting that the 90deg bending of the axons shows up nicely by the decline of the function for angles greater 90deg.
> The bending itself is reflected by the plateau between 20deg and 90deg.
> Beyond 90deg the orientations are less regular.
>
> The generation of the Orientation Salience Function is done with ImageJ by use of a dedicated plugin (cf. the 2013 report) and a macro.
>
> I shall write you off-list tomorrow for more details.
>
> Best
>
> Herbie
>
> :::::::::::::::::::::::::::::::::::::::::::
> Am 23.03.17 um 12:58 schrieb Eric Denarier:
>> Hi Herbie,
>>
>> Thanks for you help. Image is  actually Dorsal Root Ganglia neurons
>> grown on coverslip (part of the image).
>>
>> How did you get the the orientation Salience ? With imageJ ?
>>
>> Eric Denarier
>> Grenoble Institut des Neurosciences
>> Inserm U1216
>> Chemin Fortuné Ferrini
>> 38700 La Tronche
>> France
>>
>> Tél :[phone]
>>
>> http://neurosciences.ujf-grenoble.fr/
>>
>> Le 23/03/2017 à 10:12, Herbie a écrit :
>>> orientation salience function
>>
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