From GALILEOS to ImageJ
May 7, 2013 9:55 AM Subscribe
Recently I had some dental work done which included a CT scan of my teeths. I want to create little rotating 3D images from the output but I've come across some problems.
Before I went in and got the scan I was talking to my friend who said ImageJ is a free public domain software that can basically do everything I want, and he's used it many times to do this kind of thing. Awesome!
When I got the scan it was via a GALILEOS imaging system. I watched the periodontist interact with the software, it was really fascinating, and I asked for my take-home DVD of my scan, which I received.
The DVD came with the GALILEOS viewer software ready to install (available to download here along with a sample data set). I installed it, played with it, all works well.
... except I can't find a way to export the information so that ImageJ can read it. I talked to my friend about this and he'd never seen CT scan info that couldn't be read by ImageJ. His last comment on the subject was this:
"ImageJ can parse out almost anything, and has Input/Output plugins for most popular scanners - and you can always import RAW data if you know the bit depth and file dimensions.
The XML file that came with the data set I have gives a dimension of 512 x 1753 - but none of the individual files hold enough data to make an image that size.
Interesting."
and since then neither he nor I have been able to figure it out. So, my question to you is: have you personally been able to extract GALILEOS data and feed it into any other software? Do you have any idea, viewing the sample data set, how I might do this?
Playing with GALILEOS is fun, but I want to use ImageJ to create an animated .gif and that's something that GALILEOS just won't do. I can't even hide the HUD and do frame-by-frame screenshots or anything.
Before I went in and got the scan I was talking to my friend who said ImageJ is a free public domain software that can basically do everything I want, and he's used it many times to do this kind of thing. Awesome!
When I got the scan it was via a GALILEOS imaging system. I watched the periodontist interact with the software, it was really fascinating, and I asked for my take-home DVD of my scan, which I received.
The DVD came with the GALILEOS viewer software ready to install (available to download here along with a sample data set). I installed it, played with it, all works well.
... except I can't find a way to export the information so that ImageJ can read it. I talked to my friend about this and he'd never seen CT scan info that couldn't be read by ImageJ. His last comment on the subject was this:
"ImageJ can parse out almost anything, and has Input/Output plugins for most popular scanners - and you can always import RAW data if you know the bit depth and file dimensions.
The XML file that came with the data set I have gives a dimension of 512 x 1753 - but none of the individual files hold enough data to make an image that size.
Interesting."
and since then neither he nor I have been able to figure it out. So, my question to you is: have you personally been able to extract GALILEOS data and feed it into any other software? Do you have any idea, viewing the sample data set, how I might do this?
Playing with GALILEOS is fun, but I want to use ImageJ to create an animated .gif and that's something that GALILEOS just won't do. I can't even hide the HUD and do frame-by-frame screenshots or anything.
OsiriX worked well for me (or about as well as you can expect for medical software), if you have a Mac. In my case, my CAT scan was just a series of DICOM (.DCM) images.
posted by neckro23 at 2:04 PM on May 7, 2013
posted by neckro23 at 2:04 PM on May 7, 2013
I've gotten research MRIs, but they use eFilm software (the version on the CD is eFilmLt.exe).
ImageJ can import/open just about anything. If you browse the DVD, are there any folders filled with a series of files, maybe 136kb-ish big (or at least, all the same or about-the-same size)? They may very well not have a file extension. There may also be other folders with a single file which is an image, but not part of the "stack."
Drag'n'drop those files into ImageJ and they'll open (just tested with mine), and you can save them individually into whatever format you want. There's probably a way to batch it, but for a one-off... You can then use those files in a animated-GIF-maker or something. There's probably a plugin to make aGIFs with ImageJ, but I've not worked with it. ImageJ can make "stacks" but those won't display properly on the web.
posted by porpoise at 7:58 PM on May 7, 2013
ImageJ can import/open just about anything. If you browse the DVD, are there any folders filled with a series of files, maybe 136kb-ish big (or at least, all the same or about-the-same size)? They may very well not have a file extension. There may also be other folders with a single file which is an image, but not part of the "stack."
Drag'n'drop those files into ImageJ and they'll open (just tested with mine), and you can save them individually into whatever format you want. There's probably a way to batch it, but for a one-off... You can then use those files in a animated-GIF-maker or something. There's probably a plugin to make aGIFs with ImageJ, but I've not worked with it. ImageJ can make "stacks" but those won't display properly on the web.
posted by porpoise at 7:58 PM on May 7, 2013
Ok, just drag'n'dropped all the images in that folder into ImageJ.
[Toolbar] Image -> Stacks -> Images to Stack to create a stack.
[Toolbar] Save As Animated GIF.
posted by porpoise at 8:13 PM on May 7, 2013
[Toolbar] Image -> Stacks -> Images to Stack to create a stack.
[Toolbar] Save As Animated GIF.
posted by porpoise at 8:13 PM on May 7, 2013
Response by poster: zippy: "Maybe give that a shot?"
I was unable to run OsiriX because it's for a version of Mac OS X higher than I currently run. Anyway, I got the impression that OsiriX worked on DICOM data which GALILEOS doesn't support.
cjelli: "maybe the DVD you got was made such that the export was intentionally only designed to be viewed with the bundled software, not exported."
That has been my impression as well. I believe the vendors of GALILEOS feel they're doing their clients (or more accurately, their clients' clients) a favor by making this easy-to-run viewer / data set burnable CD. I saw 'export' options grayed out in the menus, so obviously that's available to the users of the full version.
neckro23: "In my case, my CAT scan was just a series of DICOM (.DCM) images."
Unfortunately (as cjelli noted) GALILEOS won't export to DICOM.
porpoise: "ImageJ can import/open just about anything."
Except, in my sad experience, the GALILEOS output.
posted by komara at 8:49 PM on May 7, 2013
I was unable to run OsiriX because it's for a version of Mac OS X higher than I currently run. Anyway, I got the impression that OsiriX worked on DICOM data which GALILEOS doesn't support.
cjelli: "maybe the DVD you got was made such that the export was intentionally only designed to be viewed with the bundled software, not exported."
That has been my impression as well. I believe the vendors of GALILEOS feel they're doing their clients (or more accurately, their clients' clients) a favor by making this easy-to-run viewer / data set burnable CD. I saw 'export' options grayed out in the menus, so obviously that's available to the users of the full version.
neckro23: "In my case, my CAT scan was just a series of DICOM (.DCM) images."
Unfortunately (as cjelli noted) GALILEOS won't export to DICOM.
porpoise: "ImageJ can import/open just about anything."
Except, in my sad experience, the GALILEOS output.
posted by komara at 8:49 PM on May 7, 2013
This thread is closed to new comments.
I was able to open the scans with OsiriX (comes in OS X and iOS flavors). Maybe give that a shot?
posted by zippy at 10:57 AM on May 7, 2013