Increasing detail on dark images

imagej
tadpole

#1

Hello,

I am new to image J. I basically have black on white images of tadpoles and I would like to increase detail/contrast to allow more precise body shape measurements. The photos are taken from above and because the organism is so dark, I cannot see the demarcations of certain body features to be able to measure them. Any help/suggestions would be much appreciated.

Thanks!


#2

@mprobins Welcome to the forum!

Could you please post a sample image?

The very first thing to try is Shift+C to open the Brightness/Contrast dialog, and adjust the display that way. You can also apply different lookup tables in Image :arrow_forward: Lookup Tables which can help to see differences more clearly. A personal favorite of mine is Fire.


#3


#4

Here’s an example. The tail extends a bit beyond the body (toward the anterior end), but without more clarity or detail, you can’t see where it extends to.


#5

Dear,

you could try taking the logarithm of the image.

In my opinion the spatial resolution at least of the sample image is poor.

HTH

Herbie


#6

Thanks @mprobins. I think the shadow is actually the hardest part, along with the blue ruler.

Nonetheless, you can get a pretty decent segmentation by thresholding the blue channel and using the Minimum auto-threshold method.

Here is a macro I built up using the Macro Recorder:

run("Duplicate...", "title=tmp");
run("Split Channels");
close("tmp (red)");
close("tmp (green)");
selectWindow("tmp (blue)");
setAutoThreshold("Minimum dark");
run("Create Mask");
run("Invert");
run("Close-");
roiManager("reset");
run("Analyze Particles...", "size=1000-Infinity add");
close();
close();
setOption("Show All", true);

As for segmenting within the tadpole itself, I agree with @Herbie that the spatial resolution is not high enough for that. See the Principles page.


#7

Thanks for your suggestions. Both the fire table and log improve the detail a bit. The sample image provided is indeed of poor resolution; these early images are the hardest to work with as the tadpoles were newly hatched and very small. Later images, where tadpoles were larger, are much easier to view.

I will keep tinkering with the image.