Re: Compare Images to Quantify Cleaning Performance

Posted by gankaku on Oct 01, 2015; 9:51am
URL: http://imagej.273.s1.nabble.com/Compare-Images-to-Quantify-Cleaning-Performance-tp5014503p5014516.html

Hi Frank,

joining the opinion and statement of Peter, I would also suggest to try to
improve imaging as much as possible for equal conditions.
Having said this, the following macro does the job quite well. I would run
it in Fiji since you need the Linear Stack alignment with SIFT plugin from
Stephan Saalfeld, thus using SIFT as suggested by Peter which is installed
by default in Fiji.
It aligns the images scale and orientation wise. Note, this affects pixels
to some extend. So, I would be careful afterwards with absolute pixel
intensity or color difference comparison (avtually I wouldn't do it).

Nevertheless, this method enables you to see where you have objects left or
washed off the plate. The difference will show you changes between the
plates. It does not distinguish if something was present first and then
washed off or was not present but appeared after treatment (which I guess
in your case is rather unlikely).

How to:

open the two images you want to compare (and only those two since the macro
is not adjusted to run on specifically selected images so far)
Copy the macro in Fijis' scripting editor (>Plugins >New >Macro) and hit
the run button.

//macro start ------------------------

run("Images to Stack", "method=[Copy (center)] name=Stack title=[]");
run("Linear Stack Alignment with SIFT", "initial_gaussian_blur=1.60
steps_per_scale_octave=3 minimum_image_size=64 maximum_image_size=1024
feature_descriptor_size=4 feature_descriptor_orientation_bins=8
closest/next_closest_ratio=0.92 maximal_alignment_error=1 inlier_ratio=0.05
expected_transformation=Affine interpolate");
run("Duplicate...", "duplicate");
run("Stack to Images");
imageCalculator("Difference", "Aligned-0001","Aligned-0002");
close("Aligned-0002");

//macro end ------------------------



Hope this helps you a little further.
Kind regards,
Jan

2015-10-01 10:11 GMT+02:00 Frank Robson <[hidden email]>:

> Hello everyone,
>
> thank you for the answers.
> Here are some sample images of the test plates before and after the
> cleaning
> process:
> <http://imagej.1557.x6.nabble.com/file/n5014514/V6vz.jpg>
> <http://imagej.1557.x6.nabble.com/file/n5014514/V6n1z.jpg>
> The distance between plate and camera is always kept the same, however the
> angle might differ. I built a kind of blackbox so that no external lighting
> will infer (the camera is always kept in manual mode).
> I'll have a look if it would be possible to use a tripod in order to assure
> a constant angle for the camera.
>
> Cheers,
> Aaron
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Compare-Images-to-Quantify-Cleaning-Performance-tp5014503p5014514.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
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