Increasing detail on dark images

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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.



@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.



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.



you could try taking the logarithm of the image.

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




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("Analyze Particles...", "size=1000-Infinity add");
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.


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.