Posted by
Leon Espinosa-3 on
Feb 06, 2014; 8:49am
URL: http://imagej.273.s1.nabble.com/How-to-quantify-a-regular-arrangement-on-my-images-tp5006427p5006432.html
Dear Christophe, I have tried an approach based on the eucledian distance and skeleton analysis. The idea is that the "band pattern" should generate bands structures in an eucledian image map and will show longer branchs in the skeleton structure:
- make intensity mask
- make the exact eucledian distance map (in fiji plugin ; process/signed eucledian exact diastance)
- make a mask with a distance threshold (the same for both conditions)
- skeletonize
- G. Landini plugin Morphologie/Binary connectivity
- Quantify the ratio branch/total (= threshold(3,3) / threshold(1,255) )
In my hands with the exemple images I have found
image1
1113/1524 = 0.73
image2
534/834 = 0.64
delta=13%
Other measures of the branch objects (Binary connectivity, threshold(3,3)):
size
image1 = 5.95 (sd = 5.23)
image2 = 4.76 (sd = 4.27)
delta=20%
AR (espect ratio)
image1 = 3,36 (sd 1,978)
image2 = 2,86 (sd 1,639)
delta=15%
Hope it helps...
Leon
Leon Espinosa
[hidden email]
Plateforme de Biophotonique Appliquée à la Microbiologie
LCB CNRS UMR7283
31, Chemin Joseph AIGUIER
13009 MARSEILLE
Tel : 04 91 16 43 28
Cell : 06 79 25 97 40
Tel sécr.: 04 91 16 40 77
Fax : 04 91 71 89 14
Le 5 févr. 2014 à 17:11, Christophe Leterrier a écrit :
> Dear ImageJists,
>
> I have images from immunocytochemistry (proteins labeled with an antibody
> in a cell culture), and I'd like to quantify a striking feature: one of the
> proteins is periodically organized (see Image1.tif), whereas the other
> seems to be more randomly clusterized (see Image2.tif). The exemple images
> are a crop of the whole image, but basically this is the pattern for the
> whole labeled structure.
>
> I'd like to analyze and quantify how "band-like" is the pattern, i.e. a
> number that would be a measure of the labeling disorder, from completely
> periodic to completely random. I don't know how to do it. I tried the
> OrientationJ and Directionality plugins, but they seem to find orientations
> in both cases, and I'm more interested in the intensity of the organization
> than in the directions of the pattern.
>
> If you have any advice on how to do this, that would be great!
>
> Thanks for your help,
>
> Christophe
>
> P.S. In case the attachments are stripped, you can find the images here:
> Image1.tif:
http://www.cleterrier.net/up/Image1.tif> Image2.tif:
http://www.cleterrier.net/up/Image2.tif>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> <Image1.tif><Image2.tif>
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