Morphometric Batch Analysis using Fish Photos

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Morphometric Batch Analysis using Fish Photos

Lourdes Lastra Díaz
Hi!
I am very new to the software, using it to do a morphometric analysis of
Fish photos. We collected a great amount of this type of photos, but image
J or Fiji doesn't quite recognize any type of fish in a binary mode. I was
looking to run a Macro, but I can't run a batch sequence to measure the
length of the different types of fish we collected since the program
doesn't quite recognize the surface or different types of scales and colors
of the Fish. I have run many possibilities if there are any suggestions it
will be very helpful.

Lourdes Lastra
[image: 2019.01.15-16.11.54-2.08.jpg][image: Screen Shot 2019-04-10 at
12.03.18 AM.png]

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*Lourdes B Lastra Diaz*
787-358-3220
email: [hidden email]

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Re: Morphometric Batch Analysis using Fish Photos

Aryeh Weiss
Here is a macro that finds the fish in your posted image.


selectWindow("2019.01.15-16.11.54-2.08.jpg");  // assumes your image is
open and so named
run("Split Channels");
close("2019.01.15-16.11.54-2.08.jpg (green)");
close("2019.01.15-16.11.54-2.08.jpg (blue)");
selectWindow("2019.01.15-16.11.54-2.08.jpg (red)");
makeRectangle(6, 244, 2028, 980);   // work on the black area only.
run("Crop");
run("3D Hysteresis Thresholding", "high=128 low=50 labelling");
setAutoThreshold("MaxEntropy dark");
setOption("BlackBackground", true);
run("Convert to Mask");
run("Fill Holes");
run("Find Edges");   // now just show that it works
run("Merge Channels...", "c1=[HystLabel_2019.01.15-16.11.54-2.08.jpg
(red)] c4=[2019.01.15-16.11.54-2.08.jpg (red)] create keep");

Once you have that you should be able to make any morphological
measurements that you need.

The hysteresis thresholding is part of the mcib 3D-suite, and you
shouldbe able to get it by setting the appropriate update site in Fiji,
or manually from
http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start

Hope this helps
--aryeh

On 10/04/2019 7:20, Lourdes Lastra Díaz wrote:

> Hi!
> I am very new to the software, using it to do a morphometric analysis of
> Fish photos. We collected a great amount of this type of photos, but image
> J or Fiji doesn't quite recognize any type of fish in a binary mode. I was
> looking to run a Macro, but I can't run a batch sequence to measure the
> length of the different types of fish we collected since the program
> doesn't quite recognize the surface or different types of scales and colors
> of the Fish. I have run many possibilities if there are any suggestions it
> will be very helpful.
>
> Lourdes Lastra
> [image: 2019.01.15-16.11.54-2.08.jpg][image: Screen Shot 2019-04-10 at
> 12.03.18 AM.png]
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051

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