7 ms·

If you download the video and extract the frames (like, with ffmpeg), and load it into 3d Slicer (slicer.org), you can actually get a 3D reconstruction out of i

by bonyt 5y ago

If you download the video and extract the frames (like, with ffmpeg), and load it into 3d Slicer (slicer.org), you can actually get a 3D reconstruction out of it! Out of a youtube video of the slices! https://i.imgur.com/wmPQvfn.jpg https://i.imgur.com/wmPQvfn.jpg

DaftDank 5y ago
I wonder if this would work for my hospital CT scans I've had in the last ~5 years. They all come on a CD, with a software program loaded onto it with the scans to view it in. It would be cool to be able to 3d visualize it all
- Pigalowda 5y ago
  Don’t go through that much trouble! There’s an easier solution. You can download free radiology viewers RadiAnt (windows compatible) or Osirix (Mac compatible). Your imaging is in DICOM format probably and you can use Radiant to export all of your slices into .jpg if you want. You can also do 3D reconstructions of soft tissue, bone, lung, etc.
  - lostlogin 5y ago
    Horos (Mac) is another - I think it’s the freeware version of Osirix. You can find InteleViewer if you hunt about as well (Mac and PC).
  - dylan604 5y ago
    >Don’t go through that much trouble! You realize this is HN where readers pride themselves on the trouble that can be accomplished in a weekend. >There’s an easier solution. But what else is one to do at the weekend?
    - spookthesunset 5y ago
      Try to turn it into an stl file, slice it and print it :-)
      - dylan604 5y ago
        Do this with a couple of "perfect" pumpkin shapes. Create a way to 3D print these as a mold to make your own "pumpkins" to be carved without all of the mess and able to last longer through the season. No more petroleum jelly, no more soaking them in the tub.
        idiotsecant 5y ago
        >No more petroleum jelly, no more soaking them in the tub. What. I feel like I am missing out on a whole field of pumpkin science here that I was unaware of.
        dylan604 5y ago
        It's a plant. Think of it as a cut flower. After cutting open a pumpkin, they are obviously no longer sealed. They start to dry out. You can rub petroleum jelly all over the carved sides to help slow down the drying out. You can also soak them in the tub, and they will pull in some of the water to help them come back into shape. There's all sort of things you can do to prolong things once they've been cut/carved/etc. My mom was a florist and designer. I've been in/around productions requiring things to be preserved so items can be kept around as long as possible. You just kind of pick up a thing or two
        Turing_Machine 5y ago
        There are also various chemical solutions that you can put on the pumpkin to make it last longer. However those are not recommended if wildlife is around. Moose, in particular, love pumpkins. I suspect deer are the same.
        dylan604 5y ago
        Sure the deer, but I don't want that stuff around me. Better living through chemistry is something I'm trying to avoid now that I can make my own choices about what goes in, on, or around me.
  - wtallis 5y ago
    The program in question (3D Slicer) is also one of those easier solutions. It can load DICOM files directly.
  - QuercusMax 5y ago
    You can get aeskulap on Linux. It's not anything that would be usable by a radiologist, but I've used it on occasion to look at some images.
- hprotagonist 5y ago
  there are many DICOM viewers available, ranging from the fairly horrible plugins for imageJ to very sophisticated things with maya or COMSOL or whatnot. OSIRX is often very good, though not free.
  - azalemeth 5y ago
    Horos is the FOSS version of Osirix and based on the same original codebase, which lives on Github – c.f. https://horosproject.org/download-horos/ https://horosproject.org/download-horos/
    - xvilka 5y ago
      Sadly, it's MacOS-only. Would be nice to have something Qt or GTK-based.
      - wazoox 5y ago
        There are many free DICOM viewer in the Ubuntu/Debian/Pop_OS repositories. I don't remember which one I used, but at least some of them allow to visit your organs in 3D :)
        figomore 5y ago
        I recommend InVesalius. It’s in Flathub (https://flathub.org/apps/details/br.gov.cti.invesalius https://flathub.org/apps/details/br.gov.cti.invesalius)
- manucorporat 5y ago
  We have been working on an open source tech that works in the browser and render 3D CTs and MRIs without installing any software, check it out: https://openview.health https://openview.health
  - sleepy_keita 5y ago
    That is really nice. Thanks for sharing!
  - roywiggins 5y ago
    fyi you've misspelled "HIPAA" on that page
  - DaftDank 5y ago
    Cool, thanks for the link.
- nick__m 5y ago
  When my wife when through invasive breast cancer some years ago¹, I got started with RadiAnt because it's easy to construct a nice looking3d reconstruction, but I quickly hit a ceiling what I was able to accomplish. With slicer I was able to produced compelling pictures to highlight the objects of interest by using custom color scales and transparency. For fun I also followed some tutorial on bone segregation for 3d printing, something that is clearly beyond the reach of RadiAnt. Still, I would recommend to learn the basics in RadiAnt by trying to see what is in the written radiologist report². You will have to learn quite a bit of arcane terminology but I found that process quite rewarding and strangely empowering. 1- 3 years after her last treatment she is still cancer free, I hope it stays that way... 2- Ask for a copy of the report when you get the DICOM DVD. If the scan was taken at a hospital they will probably redirect you to the medical archives and it assuredly won't be ready when you get the DVD but they can mail it to you.
- BadInformatics 5y ago
  You're in luck, because (assuming the scans are in a compatible format), this is exactly what 3D Slicer was designed for.
deleted 5y ago
[deleted]
anewlanguage 5y ago
I work with large-scale neuroscience imaging, and this is exactly how we compress 3D image stacks (i.e. 3d volumes) captured with confocal microscopes. Since adjacent frames are usually quite similar, there's a ton of redundancy that H.265 can exploit, and the compression ratios are amazing. For multi-channel volumetric imaging, we use ffmpeg to encode each channel as a movie and then combine all the channels into a single HDF5 file.
- andbberger 5y ago
  FIJI plugin?
  - anewlanguage 5y ago
    Yes: https://github.com/fiji/H5J_Loader_Plugin https://github.com/fiji/H5J_Loader_Plugin
    - andbberger 5y ago
      Ah, I should have guessed, I've done my time on the farm
- trombonechamp 5y ago
  Oh wow, this is a great idea. How do you deal with the lossy compression? There must be a lossless codec which uses the redundancy better than deflate?
  - anewlanguage 5y ago
    This format is meant for visualization in 3d, and even though it's lossy, it's "visually lossless" for humans. We to start with the archived lossless stacks (compressed with bz2) for any reprocessing. What you're suggesting with a lossless movie codec would be a great addition, we just haven't had the need for it yet.
- robocat 5y ago
  Do you get 3D compression artifacts? I love the idea that you rotate a spacial dimension into a time dimension, and after decompression you get artifacts from the time dimension visualised in a space dimension again.

by bonyt 5y ago

DaftDank 5y ago

I wonder if this would work for my hospital CT scans I've had in the last ~5 years. They all come on a CD, with a software program loaded onto it with the scans to view it in. It would be cool to be able to 3d visualize it all

Pigalowda 5y ago
Don’t go through that much trouble! There’s an easier solution. You can download free radiology viewers RadiAnt (windows compatible) or Osirix (Mac compatible). Your imaging is in DICOM format probably and you can use Radiant to export all of your slices into .jpg if you want. You can also do 3D reconstructions of soft tissue, bone, lung, etc.
- lostlogin 5y ago
  Horos (Mac) is another - I think it’s the freeware version of Osirix. You can find InteleViewer if you hunt about as well (Mac and PC).
- dylan604 5y ago
  >Don’t go through that much trouble! You realize this is HN where readers pride themselves on the trouble that can be accomplished in a weekend. >There’s an easier solution. But what else is one to do at the weekend?
  - spookthesunset 5y ago
    Try to turn it into an stl file, slice it and print it :-)
    - dylan604 5y ago
      Do this with a couple of "perfect" pumpkin shapes. Create a way to 3D print these as a mold to make your own "pumpkins" to be carved without all of the mess and able to last longer through the season. No more petroleum jelly, no more soaking them in the tub.
      - idiotsecant 5y ago
        >No more petroleum jelly, no more soaking them in the tub. What. I feel like I am missing out on a whole field of pumpkin science here that I was unaware of.
        dylan604 5y ago
        It's a plant. Think of it as a cut flower. After cutting open a pumpkin, they are obviously no longer sealed. They start to dry out. You can rub petroleum jelly all over the carved sides to help slow down the drying out. You can also soak them in the tub, and they will pull in some of the water to help them come back into shape. There's all sort of things you can do to prolong things once they've been cut/carved/etc. My mom was a florist and designer. I've been in/around productions requiring things to be preserved so items can be kept around as long as possible. You just kind of pick up a thing or two
        Turing_Machine 5y ago
        There are also various chemical solutions that you can put on the pumpkin to make it last longer. However those are not recommended if wildlife is around. Moose, in particular, love pumpkins. I suspect deer are the same.
        dylan604 5y ago
        Sure the deer, but I don't want that stuff around me. Better living through chemistry is something I'm trying to avoid now that I can make my own choices about what goes in, on, or around me.
- wtallis 5y ago
  The program in question (3D Slicer) is also one of those easier solutions. It can load DICOM files directly.
- QuercusMax 5y ago
  You can get aeskulap on Linux. It's not anything that would be usable by a radiologist, but I've used it on occasion to look at some images.
hprotagonist 5y ago
there are many DICOM viewers available, ranging from the fairly horrible plugins for imageJ to very sophisticated things with maya or COMSOL or whatnot. OSIRX is often very good, though not free.
- azalemeth 5y ago
  Horos is the FOSS version of Osirix and based on the same original codebase, which lives on Github – c.f. https://horosproject.org/download-horos/ https://horosproject.org/download-horos/
  - xvilka 5y ago
    Sadly, it's MacOS-only. Would be nice to have something Qt or GTK-based.
    - wazoox 5y ago
      There are many free DICOM viewer in the Ubuntu/Debian/Pop_OS repositories. I don't remember which one I used, but at least some of them allow to visit your organs in 3D :)
      - figomore 5y ago
        I recommend InVesalius. It’s in Flathub (https://flathub.org/apps/details/br.gov.cti.invesalius https://flathub.org/apps/details/br.gov.cti.invesalius)
manucorporat 5y ago
We have been working on an open source tech that works in the browser and render 3D CTs and MRIs without installing any software, check it out: https://openview.health https://openview.health
- sleepy_keita 5y ago
  That is really nice. Thanks for sharing!
- roywiggins 5y ago
  fyi you've misspelled "HIPAA" on that page
- DaftDank 5y ago
  Cool, thanks for the link.
nick__m 5y ago
When my wife when through invasive breast cancer some years ago¹, I got started with RadiAnt because it's easy to construct a nice looking3d reconstruction, but I quickly hit a ceiling what I was able to accomplish. With slicer I was able to produced compelling pictures to highlight the objects of interest by using custom color scales and transparency. For fun I also followed some tutorial on bone segregation for 3d printing, something that is clearly beyond the reach of RadiAnt. Still, I would recommend to learn the basics in RadiAnt by trying to see what is in the written radiologist report². You will have to learn quite a bit of arcane terminology but I found that process quite rewarding and strangely empowering. 1- 3 years after her last treatment she is still cancer free, I hope it stays that way... 2- Ask for a copy of the report when you get the DICOM DVD. If the scan was taken at a hospital they will probably redirect you to the medical archives and it assuredly won't be ready when you get the DVD but they can mail it to you.
BadInformatics 5y ago
You're in luck, because (assuming the scans are in a compatible format), this is exactly what 3D Slicer was designed for.

deleted 5y ago

[deleted]

anewlanguage 5y ago

I work with large-scale neuroscience imaging, and this is exactly how we compress 3D image stacks (i.e. 3d volumes) captured with confocal microscopes. Since adjacent frames are usually quite similar, there's a ton of redundancy that H.265 can exploit, and the compression ratios are amazing. For multi-channel volumetric imaging, we use ffmpeg to encode each channel as a movie and then combine all the channels into a single HDF5 file.

andbberger 5y ago
FIJI plugin?
- anewlanguage 5y ago
  Yes: https://github.com/fiji/H5J_Loader_Plugin https://github.com/fiji/H5J_Loader_Plugin
  - andbberger 5y ago
    Ah, I should have guessed, I've done my time on the farm
trombonechamp 5y ago
Oh wow, this is a great idea. How do you deal with the lossy compression? There must be a lossless codec which uses the redundancy better than deflate?
- anewlanguage 5y ago
  This format is meant for visualization in 3d, and even though it's lossy, it's "visually lossless" for humans. We to start with the archived lossless stacks (compressed with bz2) for any reprocessing. What you're suggesting with a lossless movie codec would be a great addition, we just haven't had the need for it yet.
robocat 5y ago
Do you get 3D compression artifacts? I love the idea that you rotate a spacial dimension into a time dimension, and after decompression you get artifacts from the time dimension visualised in a space dimension again.