Export XZ Orthogonal Images

Hi, I am new to Fiji and I am in need of a little help. I have DICOM file of B-Scan images (from OCT). I am interested in the XZ images of the DICOM. I can create the Orthogonal Views (Image->Stacks->Orthogonal Views) but now I would like to export all the XZ images as either individual files or its own image stack. Lastly, it would be great to create an AVI moving though the XZ images (but that would be a nice to have at this point).

I have searched the forums and the menus but still can’t seem to find a solution. Thanks in advance for any help or advice.

Hi @jpod,

Welcome to the forum.

For the first part, have a look at Image > Stacks > Reslice.

Once you have your XZ image stack, Save As > AVI... will get you the movie you want.

John

2 Likes

Thank you so much. Worked great.

Really appropriate the help.

2 Likes

Hi, if I do Image > Stacks > Reslice. it’s the sagittal view who appear, what to do to export frontal view please.

@Amiraaa,

Changing Start at: option to something different than the default (Top) will get you other kinds of orthogonal views.

John

2 Likes

Hi There, I have a question please. I am a complete novice on ImageJ (Fiji) and just signed up to this forum, so please have some patience :slight_smile: I have opened up an image of a CT scanned rock sample. I imported the Dicom files into ImageJ as an image sequence. I opened up the orthogonal views (YZ and XZ). When trying to save these images as Tiffs and then opening the image, the image is just black. However, when saving them as a jpg they open and show the image perfectly. Is there something I am doing wrong?

Thanks Andy

Hi @AndyAberdeen,

The way your images look may depend on the bit-depth of your original images and your re-saved images. (The info bar at the top of your image window will tell you what type your image is).

You can try changing the brightness and contrast for the image that appears black. It may just be that the range of values that imagej is displaying is off…

John

thank you :slight_smile:

Thanks for the advice. I will try changing the contrast on other software.

Andy

@AndyAberdeen

You can do it in imageJ (follow the link).
or Image > Adjust > Brightness / Contrast

John

Hi bogovicj,

I have tried the reslice function that you mentioned. I open the stack of dicom data of CT scan images. Then I use the Orthogonal view to see the XZ window (coronal view). After that, I use reslice but all I can get is just a small window of XZ view that I could not do anything. Could you please give me some more detail about how to export the XZ orthogonal Images.
Thanks!
27|673x500

@quangbeo87,

Welcome to the forum.

“Orthogonal view” is good for looking at orthogonal views, but it’s purpose is not to “reslice the image data” (i.e. re-arrange pixel intensities in memory).

You don’t need to use Orthogonal view at all to reslice your data.
Image > Stacks > Reslice on the original volume will do the job.

John

1 Like

Thanks so much for the advice. It has worked well for me.
Additionally, is there any way to view and interact with the 3 planes of CT images at the same time. I mean something similar to the orthogonal view but we can scroll through the images and the two other view also change accordingly.
I’m sorry if the question is inappropriate.
Thanks again.

Hi, quangbeo87

I am going to introduce my plugins.
CoordinateShift and CrossSectionViewer

Please try them if you like.

hwada