[HN Gopher] Brain images just got 64 million times sharper
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Brain images just got 64 million times sharper
Author : amichail
Score : 179 points
Date : 2023-04-18 15:59 UTC (7 hours ago)
(HTM) web link (medicalxpress.com)
(TXT) w3m dump (medicalxpress.com)
| lumenwrites wrote:
| Can a technology like this at some point be used for brain
| uploads? Or like a cheaper and better version of cryonics - to
| "backup" the brain until it can be resurrected in some way?
| CatWChainsaw wrote:
| (Obligatory "in mice") but very exciting nonetheless. And not
| just brains. I'm rather excited to see literal guts at a whole
| new level of detail.
| akozak wrote:
| Lot of folks seems to be missing the fact that they slice the
| brain up afterwards and merge those scans with the MRI data.
| nick__m wrote:
| 9.4 T is quite a strong magnetic field, as it is half the
| strength of the magnetic field used for plasma confinement in
| Tokamak Energy's Demo4 facility. Scaling this technology for
| human-sized animals will likely be incredibly expensive, but the
| 5 micron accuracy is surely worth the investment.
| echo_time wrote:
| 7T is already regularly used for human research, and approval
| for human usage has been granted for 10.5T and I believe for
| 11.7T (though I'm not sure how many images they've gotten out
| of that yet).
|
| Yes it is incredibly expensive, but it is in fact already done.
| nick__m wrote:
| I am impressed by what's possible, thank you !
| westurner wrote:
| https://thedebrief.org/impossible-photonic-breakthrough-
| scie... :
|
| > _For decades, that [Abbe diffraction] limit has operated as
| a sort of roadblock to engineering materials, drugs, or other
| objects at scales smaller than the wavelength of light
| manipulating them. But now, the researchers from Southampton,
| together with scientists from the universities of Dortmund
| and Regensburg in Germany, have successfully demonstrated
| that a beam of light can not only be confined to a spot that
| is 50 times smaller than its own wavelength but also "in a
| first of its kind" the spot can be moved by minuscule amounts
| at the point where the light is confined._
|
| > _According to that research, the key to confining light
| below the previous impermeable Abbe diffraction limit was
| accomplished by "storing a part of the electromagnetic energy
| in the kinetic energy of electric charges." This clever
| adaptation, the researchers wrote, "opened the door to a
| number of groundbreaking real-world applications, which has
| contributed to the great success of the field of
| nanophotonics."_
|
| > _"Looking to the future, in principle, it could lead to the
| manipulation of micro and nanometre-sized objects, including
| biological particles," De Liberato says, "or perhaps the
| sizeable enhancement of the sensitivity resolution of
| microscopic sensors."_
|
| "Electrons turn piece of wire into laser-like light source"
| (2022) https://news.ycombinator.com/item?id=33493885
|
| Could such inexpensive coherent laser light sources reduce
| medical and neuroimaging costs?
|
| "A simple technique to overcome self-focusing, filamentation,
| supercontinuum generation, aberrations, depth dependence and
| waveguide interface roughness using fs laser processing" http
| s://scholar.google.com/scholar?start=10&hl=en&as_sdt=5,4... :
|
| > _Several detrimental effects limit the use of ultrafast
| lasers in multi-photon processing and the direct manufacture
| of integrated photonics devices, not least, dispersion,
| aberrations, depth dependence, undesirable ablation at a
| surface, limited depth of writing, nonlinear optical effects
| such as supercontinuum generation and filamentation due to
| Kerr self-focusing. We show that all these effects can be
| significantly reduced if not eliminated using two coherent,
| ultrafast laser-beams through a single lens - which we call
| the Dual-Beam technique. Simulations and experimental
| measurements at the focus are used to understand how the
| Dual-Beam technique can mitigate these problems. The high
| peak laser intensity is only formed at the aberration-free
| tightly localised focal spot, simultaneously, suppressing
| unwanted nonlinear side effects for any intensity or
| processing depth. Therefore, we believe this simple and
| innovative technique makes the fs laser capable of much more
| at even higher intensities than previously possible, allowing
| applications in multi-photon processing, bio-medical imaging,
| laser surgery of cells, tissue and in ophthalmology, along
| with laser writing of waveguides._
|
| TL Transfer Learning might be useful for training a model to
| predict e.g. [portable] low-field MRI with NIRS Infrared
| and/or Ultrasound? FWIU, "Mind2Mind" is one way to ~train a
| GAN from another already-trained GAN?
|
| From https://twitter.com/westurner/status/1609498590367420416
| :
|
| > _Idea: Do sensor fusion with all available sensors
| timecoded with landmarks, and then predict the expensive MRI
| /CT from low cost sensors_
|
| > _Are there implied molecular structures that can be
| inferred from low-cost {NIRS, Light field, [...]} sensor
| data?_
|
| > _Task: Learn a function f() such that
| f(lowcost_sensor_data) - > expensive_sensor_data_
|
| FWIU OpenWater has moved to NIRS+Ultrasound for ~ live in
| surgery MRI-level imaging and now treatment?
|
| FWIU certain Infrared light wavelengths cause neuronal
| growth; and Blue and Green inhibit neuronal growth.
|
| What are the comparative advantage and disadvantages of these
| competing medical imaging and neuroimaging capabilities?
| legerdemain wrote:
| What's the bore diameter for a 7T or a 10T magnet? All of the
| ones I've seen wouldn't be wide enough for an adult human.
| echo_time wrote:
| They are human size research (and now clinical, albeit
| limited so far) magnets, so big enough, think about 60cm.
| It's an elbow rubbing environment, but sufficient for even
| somewhat large adults. The animals magnets are super tiny,
| of course.
| legerdemain wrote:
| I see a 7T model from Siemens with a standard 60cm bore.
| Interesting!
| mysterydip wrote:
| I didn't know who Chuck Close was to appreciate the article's
| metaphor, so for those wondering: "Close was an American painter,
| visual artist, and photographer who made massive-scale
| photorealist and abstract portraits of himself and others. Close
| also created photo portraits using a very large format camera."
| FriedPickles wrote:
| Clicked on this expecting to read about an AI enhancement
| technique. Was very refreshing to read about actual hardware
| improvements.
| Loquebantur wrote:
| It's actually neither nor.
|
| They just used the MRI to _map_ a high-resolution image
| obtained via light sheet microscopy. I doubt you can do that
| with living animals. Without slicing the brain that is.
|
| The title here is highly misleading.
| tgbugs wrote:
| The number in the title is misleading but what you write here
| is also misleading.
|
| > The diffusion tensor images (DTI) @ 15 mm spatial
| resolution are 1,000 times the resolution of most preclinical
| rodent DTI/MRI. Superresolution track density images are
| 27,000 times that of typical preclinical DTI/MRI.
|
| The resolution of the raw MRI images is significantly higher,
| without that increased resolution it would be impossible to
| align the light sheet images. The light sheet images are not
| use to "improve" MRI resolution.
| kevviiinn wrote:
| Light sheet microscopy is actually pretty neat. You can use
| it on a whole brain without slicing it but not on a living
| animal. The tissue needs to go through a special fixing
| procedure first
| SquirrelOnFire wrote:
| Yeah, they kind of blow past light sheet microscopy, but I'm
| optimistic that this can still be quite useful. There are
| brain banks with already donated brains that we could use to
| learn about diseases, and I imagine many organ donors would
| be happy to have their brains sliced up for science.
| dontwearitout wrote:
| 5 micron voxels is extremely impressive. I'm excited to see
| where this goes!
| Udo wrote:
| One more leap like this and we'll be able to resolve
| individual dendrites and obtain a complete connectome.
| Combined with microscopic slices (with suitable
| immunohistological staining), we'd be getting close to
| obtaining the data necessary for brain uploading - at least
| in mice.
| scythe wrote:
| A key problem with high-res MRI in a living organism is the
| scan time. Even fast acquisition techniques like EPI require
| around 50 milliseconds per slice. But if you want good
| resolution and contrast you're doing a spin echo which takes
| quite a bit longer. At some point you run into motion blur
| caused by the mere involuntary contraction of blood vessels,
| and that's before you consider the difficulty with patient
| compliance to the directive: _" hold still"_.
| cperciva wrote:
| If you want to scan the entire organism, sure. But higher
| resolution MRI can also mean "scan a smaller part, with good
| detail, in the same amount of time". I could imagine this
| being useful for e.g. getting a high resolution image of a
| tumour after conventional imaging was used to _locate_ it.
| azalemeth wrote:
| Indeed. To say nothing of gating acquisitions to breathing,
| head motion, eye cicadas, glymphatic flow, etc.
|
| The highest resolution MR images I have (yet) obtained were
| ~20 um^3 voxels on ex vivo (human) tissue samples fixed in
| agar with Gd3+ as a dopant, scanned at 12 T on a preclinical
| scanner. The coupled vibration of the gradient set causing
| blurring in the image domain at the extremities of the FOV
| was the limiting factor. I recall I did a partial Fourier
| acquisition - as ultimately we were limited by both T2* and
| vibration - and ended up trying to do POCS on a 4096^3
| dataset and just needing tons and tons of ram to do it over
| something useful, like a weekend. Happy memories.
| Animats wrote:
| That's useful. 5 microns is very good. Probably more than is
| needed for medical purposes. Some intermediate level between
| current technology and this scale is a useful product.
| drcode wrote:
| Mice brains are a lot easier to image than human brains afaik,
| solely because they can fit into such a tiny MRI tube, with far
| simpler magnets. So if any mouse MRI tech is scaled to a human
| device, it will almost certainly have far less resolution.
| ravenstine wrote:
| And they couldn't provide a better quality JPEG...
| JackFr wrote:
| How do you measure sharpness?
|
| It's pretty impressive to say that the linear resolution
| increased 400x, but I guess at 400x it's barely even clickbait.
| It's far more impressive to cube it and claim 64000000x
| improvement.
| dosshell wrote:
| Well, do you think a 4 Megapixel camera sensor has 2x
| resolution compared to a 2 MP?
|
| If no, I agree with you, but if it indeed does... Why should we
| not compare resolution in the higest dimension here too? We
| already have a term for linear resolution, voxel size.
|
| (But yes. I agree with your clickbait argument here. Could have
| been better to use voxel size in the heading)
| SubiculumCode wrote:
| I wonder if this resolution is possible only when the fov is
| about the size of a mouse brain. Also, I bet the bore is tiny.
| However, I didnt think 9.4T was enough.
| [deleted]
| RektBoy wrote:
| Video with a title "Brain images just got 64 million times
| sharper", in 240p ...killed me, hhehehe.
| svag wrote:
| So, if the normal MRI machines are the Hubble of medical imaging,
| this new MRI machine is the James Webb of medical imaging?
| w-m wrote:
| 64e6^(1/3) = 400, in case you were wondering. So I would take it
| that clinical MRI voxels measure 2 mm (400 * 5 um) usually? The
| article does a really bad job at explaining the number from their
| headline.
| jonnycomputer wrote:
| In the research setting, if a structural MRI is being acquired
| for anatomical research, they'll go below than by more than
| half. We acquire 2mm voxel structural MRIs since we only use it
| to help us find a warp from subject space to template space in
| fMRI analysis.
| echo_time wrote:
| Clinical scanners often use 2mm isotropic voxels, or even 3.
| Clinical usage is almost a bad reference point!. Research MRI
| at ultra high field (7T) goes to 0.8mm isotropic and below (0.5
| or 0.6 is possible).
| jonnycomputer wrote:
| Such resolution will be largely wasted if the object in the
| scanner does not remain still. Humans do not remains still.
| maxmcd wrote:
| Better link with better video:
| https://today.duke.edu/2023/04/brain-images-just-got-64-mill...
| diogopublio wrote:
| love the psychedelic image and music, tech product
| announcements kind lost their souls lately
| danbruc wrote:
| I case somebody else wonders, here [1] are some electron
| microscope pictures of neurons [and other stuff] to better
| understand what 5 um voxels means. Seems about one order of
| magnitude away from being able to image all the connections.
|
| [1]
| https://www.canadiannaturephotographer.com/rberdan_scanning_...
| CamperBob2 wrote:
| That photo about halfway down the page, wow. Absolute maximum
| creepiness.
| LeifCarrotson wrote:
| > The eyes of my wife were added in the darkroom before the
| days of Photoshop and the image is titled "Donna".
|
| ...but why?
|
| The image was probably far more impactful pre-Photoshop;
| today a pocket-carried device can do that automatically,
| live, at 1080p/60fps.
| davycro wrote:
| I've always wanted to have an MRI. I want to know how it feels to
| have all of my protons reoriented by a giant magnet. Would I be
| the same person after?
| jjtheblunt wrote:
| The only thing you feel is heated a bit in my experience
| (sports injuries, torso and sinuses).
|
| However if they use contrast it might have lasting effects. I
| only had that once and swear it made me feel dopey for weeks.
| scythe wrote:
| If you had nanoparticle contrast (ferumoxytol) it very well
| could have stuck around for weeks. Gadolinium chelate
| contrast is supposed to wash out in a few days, though.
| yalue wrote:
| Having to hold perfectly still (possibly in an uncomfortable
| pose) in a giant machine that's making loud, uncanny noises for
| 20+ minutes is indeed a very bizarre, meditative experience. It
| is interesting, but, in my opinion, you're probably going to be
| happier not having the health concerns that lead to getting an
| MRI in the first place!
| cj wrote:
| I had a MRI in college as part of a psychology experiment.
|
| If you can get into one of those studies, it's a free way to
| get a picture of your brain!
|
| I think I may have skewed their results, though. MRI is a
| very meditative experience and I'm pretty sure I fell asleep
| for brief moments when I was (supposed to be) memorizing and
| recalling pictures and words they were showing me on a
| monitor as part of the university experiment.
| nuancebydefault wrote:
| Indeed it tends to be meditative, especially because you
| have nothing else to do then holding still and relax.
| sigmoid10 wrote:
| >to have all of my protons reoriented by a giant magnet
|
| Only a tiny percentage of protons will actually get excited by
| a typical MRI. Like one in a million.
| echo_time wrote:
| This is incorrect - all of the protons align along the static
| (the strong 1.5, 3 , 9.4 etc Tesla) field, some point one
| way, and some the other - but they have all shifted so that
| they line up. The excite portion is a separate step, distinct
| from the static (B0) field. edit: distinct in some ways - the
| strength of the static field determines the RF used to flip
| the protons out of alignment.
| tonymillion wrote:
| You can't feel it, and you have to stay still for a long time
| sometimes in uncomfortable positions.
|
| All the while trying not to laugh at the funny noises the
| machine makes which will blur the image and make the procedure
| even longer.
|
| It really does sound like the machine is farting sometimes...
| oh_sigh wrote:
| I've had a few. There is definitely a weird feeling I get
| inside of them at specific certain points in the process, but I
| don't know if it is from the magnetic field, or if it is from
| some really high pitch vibrations/sounds that come off the
| machine.
| gnarcoregrizz wrote:
| I've felt a bit of heat from the radio waves, especially during
| the fMRI sequence. Personally, I get a bit claustrophobic
| during brain MRIs because of the restricting face coils, and
| you have to go pretty deep into the tube. No idea why people
| get weirded out by seeing pictures of their brain. I've never
| felt that. I think its cool.
| kelseyfrog wrote:
| I've had a couple. Proton alignment is an imperceptible state.
| You're experiencing more significant neurological changes
| reading this message than having your protons reoriented.
| robopsychology wrote:
| My wife works on MRI sequencing and has pretty long (> 1
| hour) MRI scans quite often (2/3 times a week) as they all
| test each others research on themselves. She mentioned there
| are some scans where you actually do feel them and it's quite
| uncomfortable.
| nuancebydefault wrote:
| In the hospital where I went a few times, they show a relaxing
| video while the MRI is taken. You look at a projection via a
| tilted mirror close to your eyes. Once it was featuring pandas,
| it is really nice to experience the panda effect inside the
| machine. I've never been anxious about the scan.
| jlokier wrote:
| Your protons are also oriented by the Earth's magnetic field,
| and the magnets in your phone speakers. Larmor precession (the
| effect) occurs in low fields just as in high fields. The energy
| state differences from Earth's field are generally too small to
| be useful for MRI with enough quality in a reasonable time, but
| low-field MRI is a research area.
|
| I actually felt a strong sensation when I had a high resolution
| brain MRI for research, and I rather enjoyed it. It switched on
| and off a few times during the scan, and it felt a bit like
| having a back massage, or significant mechanical vibrations in
| my back, or that feeling like gentle electric currents during
| some therapies, except for switching on and off abruptly.
|
| I asked about this after the scan because I had been told you
| don't feel anything. Surely it wasn't just my imagination, from
| the noises? Was it from machine vibrations? I didn't have any
| metal in my body except amalgam fillings, and they said those
| wouldn't affect it. And, if I could feel something, perhaps it
| wasn't as harmless as they made out.
|
| They explained after, some people feel a stimulation of their
| peripheral nervous system when the RF is on, from the tens of
| kW of microwave energy beamed through the body. For a few
| people this sensation is too much, even painful, and they have
| to stop which is one reason for the patient having the
| mechanical alert button. But most people don't feel anything at
| all from the MRI, just psychological feelings associated with
| the strange noises and confinemnt.
|
| They said it's a peripheral nerve stimulation sensation, a kind
| of phantom feeling, rather than a physical effect on the body
| being sensed by the nerves. Don't ask me why I felt it in my
| back given it was a head and neck scan.
|
| I enjoyed how it felt when I didn't know what it was, as it
| felt like it might loosen up my back a bit. I was a bit
| disappointed to not feel anything the next time I had a head
| MRI, for a medical reason (thankfully nothing found). The
| research scan had twice the field strength of the medical scan,
| and presumably different RF settings. Perhaps that made the
| difference.
| scythe wrote:
| >low-field MRI is a research area.
|
| Not just a research area! Recently on the DXMP mailing list
| someone was asking about QA procedures for their 0.064 tesla
| scanner. You can buy permanent magnets that strong without
| much trouble. I was very surprised since I wasn't aware they
| were in production -- even searching Web results for "low-
| field MRI" in due diligence for this comment, I still only
| find papers and projections. Nonetheless, the Hyperfine Swoop
| exists, and you can buy it today:
|
| https://hyperfine.io/
| eevmanu wrote:
| any idea how much could "Hyperfine Swoop System" cost?
| since pricing is not public
| wincy wrote:
| The MRI didn't feel like anything. It wasn't until the
| neurologist showed me images of my brain with my eyeballs right
| there in the front that I felt like I was going to have a panic
| attack. I have no idea how regular people just laugh off stuff
| like that. Awful existential crisis level dread seeing my
| mental meat.
| anodyne33 wrote:
| Former epileptic, I've had dozens of MRs and CTs. It's rote
| for me to see and I never had a visceral reaction and in fact
| I find it pretty fascinating. The one that I do have that's a
| standout and quite shocking is my first post-lobeectomy MRI.
| There's a very noticeable void where my right temporal lobe
| (+amygdala, cerebellum and hippocampus) were resected. Great
| conversation starter.
| codethief wrote:
| Good to hear you're no longer suffering from epilepsy!
|
| Have you noticed any other changes due to your lobectomy?
| (Isn't the amygdala responsible for fear, among other
| things?)
| 13of40 wrote:
| For anyone wanting to relive that experience, you should know
| that (in the US at least) you can go to the imaging
| department at the hospital and get all of that data on a CD,
| and there's some good free software to render it. I've got a
| 3D print of my head somewhere that I made from a CT scan.
| Workaccount2 wrote:
| I did this and then realized I have no way of using a CD.
| sundarurfriend wrote:
| You can buy portable CD reader/writers for pretty cheap
| (that connect to a USB port).
| Nuzzerino wrote:
| > some good free software to render it
|
| Not going to share the name of it? :)
| echo_time wrote:
| If the images are in DICOM format, which is common, then
| dcm2niix should be able to convert them
| https://github.com/rordenlab/dcm2niix
|
| I think it can handle a few other formats as well. Once
| they are .nii(.gz) files, then mricrogl
| (https://www.nitrc.org/projects/mricrogl) should be able
| to render it - of course, for a brain scan - this would
| be your whole head. Brain extraction is performed by more
| specialized software, but that would get you started.
| ttoinou wrote:
| Noo way? My CD only contains a bunch of jpeg from the
| slices. What file format did you get ?
| rcme wrote:
| I got an MRI of my knee after my injury. It didn't seem
| significant in any way. The ultrasound of my pregnant wife
| was way crazier to me.
| macintux wrote:
| I haven't had either, but my knee is far more
| disposable/replaceable/independent of my self-identity.
| wewtyflakes wrote:
| I had a similar feeling when the doctor showed the MRI images
| going progressively deeper into my brain. It was truly
| bizarre and made me squirm in discomfort. I hadn't expected
| to feel that way.
| RobotToaster wrote:
| I found it oddly relaxing and fell asleep.
| stansler wrote:
| Would be nice to have a better resolution for a sample video on
| YouTube (https://www.youtube.com/watch?v=FtOQddvp_U4), 64 million
| times sharper, but video quality is only 240p :)
| maxmcd wrote:
| Better video: https://www.youtube.com/watch?v=Z4WvWIJCFJc
| Retric wrote:
| I don't know if they can. 240 cubed is ~14 million while a
| mouse Brian only has 8-14 million neurons.
| https://en.wikipedia.org/wiki/Mouse_brain
| detrites wrote:
| Well something isn't adding up.
|
| How can 14 million pixels be 64 million times more pixels?
|
| Were mouse brain images just one giant pixel previously?
| Retric wrote:
| > How can 14 million pixels be 64 million times more
| pixels?
|
| It's Voxels not pixels. Voxels are 3D objects so to be
| clear this particular advancement isn't 64 million (roughly
| 400 in each linear dimension^3) times better than the best
| that came before. Think 400x400 = 160,000 more pixels and
| 400 times as many slices.
|
| Also the comparison is to a "typical clinical MRI for
| humans" which not only have 10 billion neurons but also
| tend to have relatively few slices. There's little point in
| having people spend hours in a machine if a faster scan
| with fewer slices is good enough.
|
| Anyway, while the point of comparison is suspect this is
| still a major improvement over earlier methods just look at
| the by comparison low resolution images in this paper from
| 2005. https://academic.oup.com/cercor/article/15/5/639/4422
| 13?logi...
| DefineOutside wrote:
| If you render a 240p video as 4k on youtube - the bitrate
| will be much higher and it will be less compressed than if it
| is uploaded as a 240p video.
| skybrian wrote:
| This seems to be a process that can be used on _dead_ mouse
| brains.
|
| It doesn't sound like it will be used for live animals or human
| cadavers anytime soon?
| NeuroCoder wrote:
| This is interesting for basic research but this strategy is
| unlikely to ever make it to human research. We need to find ways
| of extracting more information at reasonable Tesla. 9T just isn't
| gonna make its way to clinic
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