Image analysis and denoise

imagej

#1

Hello everyone,

I am new to imagej and ct image analysis. I have a problem which is when I drag my images t imagej it does not read them (the result is a white with some black points space) but when I import them the real images appear. Can I solve this problem?
I have a very large series of images (more than 35,000 raw CT images) which requires denoising and segmentation. Should I do these for each image one by one? because in import/image sequence, the series of white images (in a very small number of images with black points) appear not the real raw ones.
Is it possible that different images have different kinds of noise?
the image is from a column of fine sands (in the uploaded image, the noise is just blurring-please let me know if I am making a mistake)

Thanks,

Esha


#2

Do l understand right; when the images are opened via importing (rather than dragging-dropping) they are displayed correctly? Do you use bio-formats(https://imagej.net/Bio-Formats)?

Possibly you could automate the process could via using macros.
Maybe this thread could be a start:

If you have not used ImageJ before, on youtube you can find nice tutorials (here a start too https://imagej.net/Introduction).


#3

Hi Danielle,

Thanks for your help. Yes, you got it right. The format of the images are in dicom and maybe that is why the software does not recognize the images. Should I chnge the format or …?

Thank you


#4

I have not worked with DICOM format before.
Perhaps this thread could be a starting point for you?


And info page:

Could you import the images via using a macro? Then you could automate the process for all images in your stack. Test your denoise / segmentation on a few of your 35000 images, and apply this to all images.Perhaps for this, the following thread could be a starting point: