Line tool

[El-Hassan Shabana]

Hi Everyone
I am starting with Figi though i use for some time ImageJ sigmented
line tool to draw objects then i measure area and intensity. With Fiji
i draw the contour of a structure with the line tool and when i
measure it i get the area of the line not the enclosed space! This
there any way to make it possible to measure the enclosed area and
intensity?
Thank you.
--
Dr. El-Hassan Shabana
MCU Université Paris Diderot
Faculté Dentaire de Garancière
Laboratoire de Physiopathologie Orale Moléculaire,
15, rue de l'école de Médecine, 75006 Paris CEDEX.

[Miso Mitkovski]

Dear Dr. Shabana:

I understood that you want to:

1. Generate regions of interest (ROIs)
2. Measure the area occupied by the respective ROI
3. Measure the mean intensity within the ROI


So, the "ROI manager" is your friend and here is a rough answer to how to
use it.

- Update to the latest version of Fiji
- Make sure you have set what you wish to have measured
- Analyze>Set Measurements
- Here, be sure you check all that you need and uncheck all that
you don't need
- On the tool bar, select, for example, the "Polygon selections" tool
(third from the left). This will generate a closed area (ROI).
- Draw the ROI
- When finished drawing the ROI, press "t" on your keyboard. This
will invoke the "ROI Manager" and save the ROI within it. You can save
multiple ROIs per image; also good idea for later when
checking modifying
your analysis.
- From within the ROI Manager, click on "Measure". This should give
you area and mean intensity.
- Be sure you have loaded/calibrated your image previously.

Ultimately, its probably good to think about automating your work. Maybe
you could start with this script (just copy it and paste it within the Fiji
script editor; File>New>Script; there... save the script to "MyScript.ijm";
the "ijm" is important). Then click on the "Run" button within the script
editor to see what happens.

run("AuPbSn 40 (56K)");
run("Set Measurements...", "area mean redirect=None decimal=3");
makePolygon(97,219,89,236,79,246,60,252,67,278,85,295,96,301,144,268,162,238,124,226);
run("Add to Manager");
roiManager("Add");
roiManager("Measure");

Have fun...
-Mišo.

Post by El-Hassan Shabana
Hi Everyone
I am starting with Figi though i use for some time ImageJ sigmented
line tool to draw objects then i measure area and intensity. With Fiji
i draw the contour of a structure with the line tool and when i
measure it i get the area of the line not the enclosed space! This
there any way to make it possible to measure the enclosed area and
intensity?
Thank you.
--
Dr. El-Hassan Shabana
MCU Université Paris Diderot
Faculté Dentaire de GaranciÚre
Laboratoire de Physiopathologie Orale Moléculaire,
15, rue de l'école de Médecine, 75006 Paris CEDEX.
--
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