Micro-CT Resources

My research takes advantage of the detailed 3-dimensional information that can be learned from micro-computed tomography (micro-CT). Below is a list of useful resources that I have compiled during my (ongoing) education and experimentation with visualization of of micro-CT scan data. Most of my work has been with OsiriX or (increasingly) Amira, and so these resources will focus on these software tools. This page is by no way exhaustive, but it helps me curate links and helpful information so maybe it will help others too.

Comments on OsiriX vs. Amira

OsiriX has the major advantage of being open source (and the 62 bit version upgrade is very cheap compared to the other options out there). It is fairly quick and easy to visualize your data using volume rendering in Osirix. Simple region growing and selection of regions of interest work well, but more complicated segmentation quickly becomes frustrating. It should be noted that OsiriX is only for Mac.

Amira’s strength seems to be in surface rendering and segmentation. I also find the working environment makes it much easier to track your manipulation history and save your progress, which are good from a practical and publication standpoint. For comparative and quantitative analysis, I am transitioning to using Amira over Osirix. Amira is expensive and only for PC, although I still use OsiriX for quick and more appealing volume rendering.

My notes

Amira — basic info about opening files and segmentation

OsiriX — basic notes about opening files, volume rendering, and ROIs

Tutorials-Amira

Segmentation and suface extraction from Brown’s XROMM resources

Tutorials-OsiriX

Quick guide to OsiriX from Stanford’s Image Quantitation, Analysis and Visualization Resources

Extract a 3D volume from a series from WikiCommons. Less useful now that the screenshots have been taken down.

Bone segmentation instructions from Brown’s XROMM resources page

Downloads

OsiriX. Mac only. Upgrade to 64-Bit version highly recommended

MicroView download from SourceForge. Useful for file manipulation and conversion (e.g., .vff –> .DCM)

Manuals

MicroView Quick Reference Guide.

4 Responses to Micro-CT Resources

  1. Declan says:

    Hi Sarah,

    Thank you for providing the information on getting started with using Amira. I am currently using your how to guide to open CFD simulations in it for post processing visualization. I am only new to it and I am having trouble with the raw data input, could you shed anymore light on how this is done?

    • sarahjlongo says:

      Hi Declan. As you can probably tell my “getting started” guide to Amira pretty much grew out of notes to myself as I dealt with my own file and file types, but I will try to help as much as possible. When you import raw ct-data you need to know the scan parameters (such as voxel size resolution, dimensions, endianness, etc) since they are not embedded in the data files you are importing (versus for instance dicom files which tell Amira all that information). In my case, when I get my ct-data back from my facility they include a .hdr (header file) or .xml that includes all this information which I then manually open to find parameters and input them into Amira. Hope that helps!

  2. Declan says:

    Thanks for the feedback Sarah. I think my main issue is I’m using data from CFD software. Specifically I’m using STAR CCM+, so my only way of opening the data is in large data mode. I have since successfully opened it in Large Data format and input the relevant information to make the requested and filesize bytes match. So I’m assuming since these now match, and the file opens, that it is correct. Once I then apply a bounding box and iso-surface etc, I basically get a small cube in the display with a number of planes with something that only looks like noise on them. Nothing representative of what my simulation is about. Now, I must say, I could be just not setting it up right once it opens, or maybe even though the file is opening, it may not be able to read it.

    Have you ever used any CAE type file inputs? or have it all been from CT images.

    Either way, thanks for your help!

  3. sarahjlongo says:

    Sorry, I have not worked with CFD or CAE data specifically so I am not going to be much help trouble shooting. If you think you are opening it correctly, then your problem could be the thresholds you are applying with the isosurface?

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