Posted by
Romain VAUCHELLES on
Apr 18, 2018; 2:43pm
URL: http://imagej.273.s1.nabble.com/Issues-with-Analyse-Particule-tp5020527.html
Dear All,
To start, I think to have found a bug (using the daily built version of
ImageJ 1.52a57) where the objects found with the "Analyze Particles..." tool
are not really matching with the threshold when applied to the following
picture:
<
https://seafile.unistra.fr/d/f8f47d8fbdf84c098971/>
https://seafile.unistra.fr/d/f8f47d8fbdf84c098971/by using the following macro code :
setAutoThreshold("MinError dark");
run("Analyze Particles...", "size=0-100 clear add");
waitForUser("a");
run("Analyze Particles...", "size=0-Infinity clear add");
Indeed, if you look (or zoom) in the bottom left corner there are clearly
some particules <100 pixels witch are not selected (as they should).
Additionally, the selection is not following the contour of the resulting
thresholded picture and even by changing (manually) the threshold
conditions, no setting is able to match with the obtained selection.
Besides this, if I want to select my tissue excluding holes, here is no
(easy) way to do this with the "Analyze Particles..." tool (or at least I
didnt find it).
Thus in order to solve this issue, I usually use the "Versatile Wand" plugin
http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start
<
http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start&s%5B%5D=wand> &s%5B%5D=wand
within a function like:
setAutoThreshold("MinError dark");
RingSelection();
function RingSelection() //need Versatile_Wand.java
http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start
{
run("Clear Results");
run("Analyze Particles...", "display
record");
for(i=0;i<nResults;i++)
{
xon=getResult("XStart",i);
yon=getResult("YStart",i);
call("Versatile_Wand_Tool.doWand",xon, yon, 0.0, 0.0, 0.0, "8-connected");
//run("Versatile Wand",
"value=0 color=0 gradient=0 connectedness=8-connected x="+xon+" y="+yon+"
do");
roiManager("Add");
}
selectWindow("Results");run ("Close");
run("Select None");
}
But this function is quite time consuming and (especially) cant be used in
batchmode (because of the use of result windows)
Thus is there an easy way to be able to exclude holes from selections?
I thank you very much in advance for your help and ideas on this.
My best regards,
Romain
--
R.Vauchelles
Ingénieur d'étude Plateforme d'Imagerie Quantitative
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http://imageriepiq.u-strasbg.fr/03 68 85 42 98 - <mailto:
[hidden email]>
[hidden email]
CNRS UMR 7021 - Laboratory of Bioimaging and Pathologies
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