Save as a .cat file

Hello all,

This is my first question about Fiji.
I made a scan with a Inveon pre-clinical microCT with 120 projections. In the post-processing, I only want to analyze the first 45 because of the contrast injection during the first 60 seconds of the scan (aprox the first 45 projections). To my knowledge,tThe software of the microCT does not support reconstruction of only a subset of the projections.
I found the source file, which is a .cat file. I can open it in imageJ and make a subset of the first 45 slices. However, i cannot save it in the original file-format .cat.
The software of the microCT only accepts .cat files, so i have to find a way to cut out the first 45 slices for reconstruction. (or find another program to do the reconstruction)

Can anybody help me saving the file as .cat (or convert for example?

Thank you all in advance!

Good day,

as far as I understand your description, you want to reconstruct an image from a limited number of projections (angles). This is known as missing cone reconstruction and in general you cannot expect reasonable results.

What do you expect from such a reconstruction?
An answer may perhaps help clarify whether your endeavor is reasonable.


Added later:
You also speak of 45 slices, so it is not quite clear whether you wish to do missing cone reconstructions or simply reconstruct a subset of slices from a series of slices.

Please resolve this issue.


Best

Herbie

Welcome to the forum!

I briefly looked into the .cat format, and it seems to be a proprietary format made by Inveon for their software.

As a rule, the Bio-Formats project does not save to proprietary formats—only open formats. And the SCIFIO project has similar guidelines as far as the core ImageJ developers are concerned—although of course, anyone is free to write a SCIFIO plugin to write whatever format they want.

So if you really need to write a .cat, you will have to create your own plugin to write the format. I found this page which has another company’s limited reverse engineered information.

But if at all possible, your best bet is to use a different file format.

Thank you for your quick replies!

The reason why I want to do a reconstruction with a limited amount of angles is as follows:
We did an contrast injection for 60 seconds, but the ‘fastest’ acquisition the microCT could make took almost 200 seconds. That means that for 140 seconds, there was no contrast injection. We would like to reconstruct the projections during the 60 seconds of contrast-injection and see if it gives a reasonable image quality.
For me, it is not specifically necessary to convert back to .cat, but i have to get reconstructions of those images. The only thing i can see now are ‘raw’ images. So does anybody know a program/plugin to reconstruct those images to ‘normal’ CT data (sagital, axial, coronal reconstructions?)

Thanks!
Thomas

Thomas.

still not quite sure if you are speaking of projections or slices.

If you are really speaking of projections, then you won’t see much if you look at a single one. (A single tomographic projection actually is a 1D-signal smeared out in the orthogonal direction.) Limited number of projections in a missing cone scenario means that from the required projections that must be taken from 0 to 180 deg those taken from an angular interval are missing. If this missing angular interval has a considerable extent, then you won’t get a reasonable resonstruction of a slice image.

Best

Herbie

Dear Herbie,

I am talking about the projections. ImageJ calls them slices i think if I open the file in there.
The scan is made over 220degrees. I want to make a reconstruction with the projections of the first 90 degrees (about 45 projections)
From one of the vendors, I’ve heard you can get a reasonable reconstruction with that amount of projections of that angle.

Best!

Dear Thomas,

thanks for clarifying the issue.

With the mentioned parameters I doubt that you will get a useful reconstruction. It’s against the mathematical principle of tomography. Of course it depends on the properties of your objects and what image quality you are after. In fact, limited angle tomography had been used before CT but image quality can’t really compare to full angle CT.

Another situation is present if the missing projections are equally distributed over the whole range of angles. In such cases it is even possible to tell how that “thinning” of projections is reflected in the reconstruction.

As far as I remember there is at least one CT plugin for ImageJ.
Just do a search on the ImageJ plugins webpage.

Best

Herbie

Dear Thomas,

just for the record concerning missing projections in CT:

  1. Missing projections of an angle interval:
    Assuming parallel beam projection, this means that object structures orthogonal to the missing projection directions will be missing in the reconstructed image.
    With fan-beam projection, the beam-rays can be re-arranged to the equivalent parallel beam projection geometry.

  2. Missing projections distributed over the total angle range (thinning):
    The sampling theorem of CT says that the required number z of parallel beam projections depends on the number of resolvable samples n along the object diameter: z >= n pi/2.
    If the number of parallel beam projections is less than z, artifacts will appear in the reconstructed image that essentially are ripple-like structures at the outer regions of the object. In short: The unaffected diameter of the reconstructed image is proportional to z < n pi/2.

In both cases the reconstructed image may be strongly affected, either by missing object structures (1) or by disturbing artifacts (2). Both effects are more severe than, e.g. lowpass effects or the like.

HTH

Herbie