When I stabilize images in ImageJ, they often become blurry. Why is this, and how do I avoid it? I performed the following steps: denoised z-stacks with Hybrid 3D Median Filter plugin; created maximum projection; then stabilized with Image Stabilizer plugin. Stabilized and unstabilized files are attached for comparison. These are 16-bit images. Thanks!
Welcome to the forum.
Something is mixed up here.
The size of rcc_denoised_only.tif is 50x50 pixel.
The size of rcc_denoised_stable.tif is 61x62 pixel.
The intensity range of rcc_denoised_only.tif is very different from size of rcc_denoised_stable.tif.
All this can not be caused by the Stabilizer.
Can you provide a macro of your complete processing.
Hi @phaub, I think I cropped them separately, so this accounts for the different sizes. I don’t always stabilize, so I would have done this in separate steps. I’ll add that these are old images that I’m looking at. I don’t have a single macro for all processing, but this is my typical workflow.
I would first denoise with this plugin: 3d Hybrid Median Filter (nih.gov)
Then I would stabilize with this plugin: Image Stabilizer - ImageJ using this text:
run(“Hybrid 3D Median Filter”, " ");
Then I would make the maximum projection.
I apologize if I’m misunderstanding what you’re asking for. I’m not very experienced with the terminology - and I’m asking to try to understand the process better. But would one of these steps alter the values?
Clarification: would one of these steps alter the intensity values? Specifically, could the stabilizer do that? I don’t believe I’ve done anything else, and this is a problem I’ve noticed before with stabilized images.
It seems as if your processing involves 3 steps
1- Hybrid 3D Median Filter
2- Image Stabilizer
3- Maximum projection
Step 1 can blur your image.
Step 3 can blur your image if the single planes are not well aligned.
Step 2 (Image Stabilzer) will alter pixel intensities. But it should not introduce significant blur.
But again, you should describe your question more specific.
The both images you have posted are not totally different in terms of ‘sharpness’. In other words: The stabilized image is not much blurred compared to the denoized version.
I don’t understand what the question really is.
Beside that, the Image Stabilzer has some options.
What are the settings you have used for processing?
Best would be if you repeat your test.
Use one of your images, switch on the MacroRecorder, processes your image and post the test image, the result image and the recorded macro. In this way it will be more easy to see what the problem is.