Scanco image files: accessibility in ImageJ/BoneJ and possibility for realigning axes

[Dave]

Hello all,

 

I have previously (and very gratefully!) used BoneJ to process clinical QCT data of human metatarsals (voxel size ~0.5mm), both from intact cadaver foot samples and in an in vivo study. One tricky thing about measuring geometric strength parameters in the metatarsals is that it's not possible to simultaneously align each metatarsal's long axis in a QCT scanner. Thus, for me the most helpful aspect of BoneJ has been the Moment of Inertia function, which permitted realignment of voxel data along each metatarsal's inertial axes. I imported the segmented metatarsal files into ImageJ, then ran the Moment of Inertia function to align the voxels with the density-weighted inertial axes.

 

This leads to my question: does anyone have experience with Scanco image files, particularly from the XtremeCT scanner? I may have access to an XtremeCT scanner for an upcoming in vivo project, and in addition to scanning the distal tibia (which seems straightforward in the XtremeCT) I would like to once again scan the metatarsals and then realign the voxel data so that I can measure cross-sectional properties. I have two main concerns:

 

- File size: while the forefoot is roughly the same circumference as the distal tibia, I would need to scan an axial length of ~100 mm or longer to capture the metatarsals. A quick back-of-the-napkin calculation makes it clear that the resulting image files would be HUGE, but capturing less than the full length of the bones would seem to eliminate the possibility of using the Moment of Inertia function to realign the voxel data.

 

- Segmentation: I have been doing segmentation with intensity-based filtering macros in ImageJ and Analyze. Does Scanco software offer segmentation? If nothing else, this would reduce the number of voxels imported into ImageJ.

 

Overall, does this idea seem possible? Any advice regarding Scanco files?

 

Many thanks.

 

-Dave 

[Michael Doube]

Hi Dave,

 

This leads to my question: does anyone have experience with Scanco image files,

Yes, Karl-Heinz Kunzelmann graciously contributed code to BoneJ (available since v1.3.8) which opens Scanco's ISQ file format, which is produced by their X-ray microtomography scanners. You can drag n drop ISQ files straight onto ImageJ and your ISQ file will just open. You will need enough RAM though. Thankfully these days it is not too expensive to equip a workstation with enough RAM to handle most studies.
 

particularly from the XtremeCT scanner?

I'm not so sure about that - does anyone here have experience with this technology? Looking at the Scanco website, it seems like ISQ is the only file format they are using, and since they market XtremeCT as "Clinical microCT", I will hazard a guess that the file format engineering has been transferred between capture technologies. Can anyone confirm?

 

- File size: while the forefoot is roughly the same circumference as the distal tibia, I would need to scan an axial length of ~100 mm or longer to capture the metatarsals. A quick back-of-the-napkin calculation makes it clear that the resulting image files would be HUGE,

How big is HUGE? 1GB, 10GB, 100GB, 1TB... The first 3 should be handled OK in a reasonable recent workstation. Actually one thing which would be nice for the ISQ reader is the possibility to open as a virtual stack, so that slices are read out only as needed. But, we haven't implemented that yet. It might have to wait for IJ2 or we might have to write the importer as a plugin for scifio (formerly Bio-Formats). Another approach might be to byte-by-byte convert ISQ into multi-page TIFF, then let ImageJ open the multi-page TIFF as a virtual stack. Any volunteers willing to implement that? ;-)

  

Overall, does this idea seem possible? Any advice regarding Scanco files?

1) Try Karl-Heinz's ISQ Reader in BoneJ and especially the option to do 2x downsampling.
2) Find a workstation with tons of RAM, and big SSDs.

Michael

[Ali Ghasem Zadeh]

Hi Dave and Michael,

I am using The XtrmeCT Scanner ( HRpQCT- Scanco)for 6 years and happy for any help.

Thanks

Ali

 

Ali Ghasem-Zadeh
Medical Physicist, MACPSEM
Endocrinology Centre of Excellence
Level 2, Centaur Building, Repatriation Hospital,
Austin Health,the University of Melbourne
Waterdale Road, West Heidelberg,
VIC 3081 Australia
Ph: +61 (3)9496 2282, 9496 2081
Fax: +61 3 9496 3365
E-mail:al...@unimelb.edu.au

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[Michael Doube]

Hi Ali,

I am using The XtrmeCT Scanner ( HRpQCT- Scanco)for 6 years and happy for any help.

What file format does your scanner produce, and have you tried opening XtremeCT files in ImageJ?

Michael

[Ali Ghasem Zadeh]

Hi Michael,

XtremeCT provides ISQ files for each batch .

 

To read the ISQ files you need install the ISQ reader in ImageJ .

Please following  the following link to find how to install it.

 

Prof. Dr. Karl-Heinz Kunzelmann

www.dent.med.uni-muenchen.de/~kkunzelm/.../index.php?...Share

Plugins>KHKs MicroCT Tools, "KHKs Scanco microCT ISQ HeaderReader..." Plugins>KHKs MicroCT Tools, ... KHKs Viff File Reader and Writer (ImageJ plugin) ...

 

 

However, for big files (more than 330 slices)I recommend ,convert ISQ files to DICOM( slice by slice) by using  XtremCT software .

 

Regards,

Ali

 

Ali Ghasem-Zadeh
Medical Physicist, MACPSEM
Endocrinology Centre of Excellence
Level 2, Centaur Building, Repatriation Hospital,
Austin Health,the University of Melbourne
Waterdale Road, West Heidelberg,
VIC 3081 Australia
Ph: +61 (3)9496 2282, 9496 2081
Fax: +61 3 9496 3365
E-mail:al...@unimelb.edu.au

 

 

 

 

[Michael Doube]

Hi Ali,

XtremeCT provides ISQ files for each batch .

Thanks for the confirmation.

 

 To read the ISQ files you need install the ISQ reader in ImageJ .

That's now bundled in BoneJ as File > Import > Scanco ISQ, since last November (v1.3.8), with a few feature enhancements (e.g. drag n drop, calibration) but without the option to convert to 8-bit.

http://bonej.org/utilities

 

However, for big files (more than 330 slices)I recommend ,convert ISQ files to DICOM( slice by slice) by using  XtremCT software .

Good advice, because DICOM support is quite mature in ImageJ, and doing it this way gives you the option to 'use virtual stack' when you import the image sequence, which helps if you have too little RAM. However, I'm not sure if the DICOM images are calibrated in the same way. One of the advantages of using the ISQ reader in BoneJ is that it automatically sets the pixel calibration to linear attenuation units (1/cm).

Michael

[Dave Gutekunst]

Hi all,

 

Many thanks for the helpful guidance. For my current computing capabilities, files >1GB would qualify as "huge." This is without a dedicated workstation for image analysis, which I will be seeking as a part of the new project, especially considering your advice. 

 

Dave 

 

 

 

 

 

 

 

[Michael Doube]

Hi Dave,

 

For my current computing capabilities, files >1GB would qualify as "huge." This is without a dedicated workstation for image analysis, which I will be seeking as a part of the new project

As an interim solution, consider buying some RAM, which has become quite cheap - something like £17 - £30 / GB for laptop RAM and ~£10 / GB for ECC-registered (workstation grade) RAM.

Michael