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| kanzure | .tw https://twitter.com/VitalikButerin/status/745107221416009728 | 06:25 |
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| yoleaux | http://www.overcomingbias.com/2016/06/unauthorized-topics.html I think uncoordinated ecosystems of human-derived brain emulations are a worthy topic of discussion. @robinhanson (@VitalikButerin) | 06:25 |
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| eudoxia | every time I see a picture of vitalik buterin I think "this guy should eat a burger" | 07:13 |
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| kanzure | eudoxia: that's your complaint? out of everything? | 07:35 |
| kanzure | eudoxia: what about his obvious role as the extended tentacle of eliezer yudkowsky?? | 07:35 |
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| kanzure | it's the territorial expansion of the lesswrong brain slugs | 07:36 |
| eudoxia | oh kanz, young people are easily deceived by poly bay area cult leaders | 07:36 |
| eudoxia | although the thought of people having been molded by LW during their formative years is troubling | 07:36 |
| kanzure | eh i suppose it's not as bad as ponyfic or somethi-- oh. | 07:37 |
| c0rw1n- | lol | 07:38 |
| eudoxia | I forgot who wrote pony fan fiction | 07:47 |
| eudoxia | was it just gwern or was it a general LW thing | 07:47 |
| kanzure | everyone? | 07:48 |
| eudoxia | yeah it was probably everyone | 07:49 |
| kanzure | "what would 4chan do" | 07:50 |
| kanzure | they would probably write anti-pony fic | 07:51 |
| eudoxia | yes | 07:51 |
| c0rw1n- | kanzure huh what where? | 08:01 |
| c0rw1n- | only lw-aligned ponyfic i know of is FiO | 08:01 |
| kanzure | ... | 08:01 |
| c0rw1n- | which is not on hte main site | 08:01 |
| kanzure | i really hate that i know that you are talking about "friendship is optimal" :( | 08:02 |
| c0rw1n- | obviously written by one of the cultits or someone familiar with the memespace | 08:02 |
| Urchin | talking about Friendship is Optimal? | 08:10 |
| Urchin | ups, I haven't read all the replies | 08:11 |
| c0rw1n- | let's not | 08:11 |
| c0rw1n- | ( uh, let's not *here* ) | 08:11 |
| Urchin | good point | 08:11 |
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| JayDugger | Seriously? LW went further downhill from HPMOR? FIO? | 08:50 |
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| nmz787_i | what is LW? | 09:07 |
| nmz787_i | oh, lesswrong? | 09:07 |
| nmz787_i | that channel was pretty boring the one or two times i popped in... i don't know why all you folks bring it up so much | 09:07 |
| xentrac | haha | 09:09 |
| chris_99 | what are they lesswrong than | 09:09 |
| xentrac | than they used to be, ieally | 09:10 |
| xentrac | ideally | 09:10 |
| xentrac | there's a large intersection between H+ interested people and lesswrong acolytes | 09:10 |
| nmz787_i | seemed like conversation I'd hear in a sports bar or something, as I recall... or no more interesting than that, at least | 09:15 |
| chris_99 | nmz787_i, can you think of anything better than using something like modular hose, to enable me to easily move about the diffraction grating by hand? | 09:17 |
| c0rw1n- | the irc is not equal to the site, it's its own little subcommunity. SRN and general quality varies a lot | 09:17 |
| c0rw1n- | *SNR | 09:17 |
| nmz787_i | chris_99: for calibration (one time) or normal operation?? | 09:21 |
| nmz787_i | i mean, are you just going to use the hose like a stick, to nudge the grating as it is sitting on a table or bench or something? | 09:21 |
| chris_99 | for normal operation sorry | 09:30 |
| nmz787_i | hrmm | 09:30 |
| nmz787_i | not sure what you're thinking | 09:31 |
| chris_99 | sec let me get a picture | 09:31 |
| nmz787_i | maybe post it to https://sketch.io/sketchpad/ or something | 09:31 |
| nmz787_i | (i just searched sketch online share) | 09:31 |
| chris_99 | http://toolguyd.com/sparkfun-third-hand-kit/ this kind of thing, and just use one hose to hold the grating | 09:31 |
| chris_99 | and the other the slit | 09:32 |
| nmz787_i | ah | 09:34 |
| nmz787_i | i was thinking garden hose | 09:34 |
| nmz787_i | or medical tubing | 09:34 |
| nmz787_i | those are the snake arm things | 09:34 |
| nmz787_i | hmm, something better | 09:35 |
| nmz787_i | yeah I guesss what fenn said, something like a kinematic stage/mount | 09:35 |
| chris_99 | aren't they expensive though? | 09:35 |
| nmz787_i | yeah, wonder if there is a 3d print model tho | 09:35 |
| chris_99 | oh yeah | 09:35 |
| chris_99 | that's a point | 09:35 |
| chris_99 | i've got a friend with a 3d printer too | 09:36 |
| nmz787_i | chris_99: http://www.thingiverse.com/thing:30727 | 09:37 |
| nmz787_i | i don't see how they get fulle steering with that | 09:38 |
| nmz787_i | seems like there is something we aren't seeing | 09:38 |
| chris_99 | that's interest | 09:39 |
| chris_99 | *interesting | 09:39 |
| chris_99 | using that metal stuff is a good plan | 09:40 |
| nmz787_i | as long as the plastic doesn't sag appreciably over the lifetime of your calibration/measurement | 09:40 |
| chris_99 | mmm | 09:41 |
| nmz787_i | i centrifuged some plastic a few days ago, apparently too fast, as it came out slightly melted on the top where there was a piece of metal | 09:41 |
| chris_99 | interesting, how did you do that, molten plastic? | 09:42 |
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| nmz787_i | nah it was just a consumer vial that had some jojoba oil in in, and I wanted to collect it all to use on a q-tip | 09:43 |
| nmz787_i | near the top just below the last thread of the screw-cap, it was smushed down a mm or so | 09:43 |
| nmz787_i | guess whatever the plastic was, is just "hard" in normal gravity at that temperature | 09:44 |
| chris_99 | oh sorry i misunderstood doh, the vial was plastic | 09:44 |
| nmz787_i | yeah | 09:44 |
| chris_99 | is that a lab centrifuge with a cover? the DIY drill one scares me heh | 09:48 |
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| nmz787_i | yeah | 10:00 |
| nmz787_i | got one on ebay, and another from a diybio guy | 10:00 |
| chris_99 | cool | 10:04 |
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| kanzure | "Rumor source obfuscation" https://arxiv.org/pdf/1412.8439.pdf | 10:39 |
| kanzure | .t https://www.youtube.com/watch?v=SKvx7VVI6IM | 10:44 |
| yoleaux | kanzure: Sorry, I don't know what timezone that is. If in doubt, see https://en.wikipedia.org/wiki/List_of_tz_database_time_zones for a list of options. | 10:44 |
| kanzure | .title https://www.youtube.com/watch?v=SKvx7VVI6IM | 10:44 |
| yoleaux | Mobisante Quick Overview.wmv - YouTube | 10:44 |
| kanzure | "The smartphone supports up to 90 minutes of continuous scanning on a full charge" | 10:45 |
| kanzure | "The tablet provides up to 2.25 hours of continuous scanning time on a full charge" | 10:45 |
| kanzure | jcline provided some good feedback. | 10:46 |
| chris_99 | is that an ultrasound scanner, if so, have you seen the DIY ultrasound scanner someones working on, that was on HaD? | 10:49 |
| kanzure | chris_99: a thing we are doing https://docs.google.com/spreadsheets/d/1BD9H9DfQBJx_a4XiDkL6AKetvqO1Sk7zneAVD5kk39E/edit | 10:52 |
| chris_99 | cool, i'll have a looky | 10:52 |
| chris_99 | what's RMB mean | 10:54 |
| kanzure | "Simple, scalable proteomic imaging for high-dimensional profiling of intact systems" http://www.sciencedirect.com/science/article/pii/S0092867415015056 | 10:54 |
| kanzure | "This method, termed SWITCH, uniformly secures tissue architecture, native biomolecules, and antigenicity across an entire system by synchronizing the tissue preservation reaction. The heat- and chemical-resistant nature of the resulting framework permits multiple rounds (>20) of relabeling. We have performed 22 rounds of labeling of a single tissue with precise co-registration of multiple datasets. Furthermore, SWITCH synchronizes ... | 10:54 |
| kanzure | ... labeling reactions to improve probe penetration depth and uniformity of staining. With SWITCH, we performed combinatorial protein expression profiling of the human cortex and also interrogated the geometric structure of the fiber pathways in mouse brains. Such integrated high-dimensional information may accelerate our understanding of biological systems at multiple levels." | 10:54 |
| kanzure | 20 rounds of labeling | 10:54 |
| chris_99 | are you not missing a psu for the piezo | 10:55 |
| kanzure | "Hippocampal calbindin-1 immunoreactivity correlate of recognition memory performance in aged mice." http://www.ncbi.nlm.nih.gov/pubmed/22503902 | 10:56 |
| kanzure | "Our results suggest that hippocampal Calb1 expression affects memory performance in aged mice probably via its role in maintaining neuronal calcium homeostasis. Alternatively, our finding of lower Calb1 immunoreactivity with poorer memory performance in aged mice might be attributed to saturation of Calb1 protein by higher levels of intracellular calcium, due to aging-related dysregulation of neuronal calcium fluxes." | 10:56 |
| kanzure | "Transcription factor Sp4 regulates expression of nervous wreck 2 to control NMDAR1 levels and dendrite patterning." https://www.ncbi.nlm.nih.gov/pubmed/25045015 | 10:57 |
| kanzure | "Mice mutant for the transcription factor Sp4 have reduced levels of NMDAR subunit 1 (NR1) protein, but not mRNA, and exhibit behavioral and memory deficits (Zhou et al., [2010] Human Molecular Genetics 19: 3797-3805). In developing cerebellar granule neurons (CGNs), Sp4 controls dendrite patterning (Ramos et al., [2007] Proc Natl Acad Sci USA 104: 9882-9887). Sp4 target genes that regulate dendrite pruning or NR1 levels are not known. ... | 10:57 |
| kanzure | ... Here we report that Sp4 activates transcription of Nervous Wreck 2 (Nwk2; also known as Fchsd1) and, further, that Nwk2, an F-BAR domain-containing protein, mediates Sp4-dependent regulation of dendrite patterning and cell surface expression of NR1. Knockdown of Nwk2 in CGNs increased primary dendrite number, phenocopying Sp4 knockdown, and exogenous expression of Nwk2 in Sp4-depleted neurons rescued dendrite number. We observed that ... | 10:57 |
| kanzure | ... acute Sp4 depletion reduced levels of surface, but not total, NR1, and this was rescued by Nwk2 expression. Furthermore, expression of Nr1 suppressed the increase in dendrite number in Sp4- or Nwk2- depleted neurons." | 10:57 |
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| kanzure | chris_99: that doc is not a complete specification | 10:59 |
| kanzure | by any stretch of salvador's imagination | 10:59 |
| chris_99 | aha | 10:59 |
| chris_99 | i have a 2mhz transducer i keep meaning to play with, the echopen stuff had a handy looking psu module | 11:00 |
| chris_99 | that they link to in their specs | 11:00 |
| xentrac | chris_99: any idea what the Q factor of the transducer's 2MHz resonance is? | 11:06 |
| FourFire | > <eudoxia> I forgot who wrote pony fan fiction | 11:07 |
| FourFire | "iceman" | 11:07 |
| FourFire | he wrote an AI-Foom thingwhich got a bunch of metafic | 11:07 |
| xentrac | I don't fully understand why ultrasound transducers usually have such enormous Q factors. I mean, is it just the large mismatch in acoustic impedance between air and the piezo? | 11:07 |
| xentrac | FourFire: an AI-Foom thing about My Little Pony? This is sounding tempting ;) | 11:08 |
| FourFire | > <kanzure> i really hate that i know that you are talking about "friendship is optimal" :( | 11:08 |
| FourFire | what is the cause of that hate specifically? | 11:08 |
| kanzure | it's valuable brain space | 11:08 |
| xentrac | nmz787_i: lesswrong isn't an IRC channel; it's a web site and a group that meets monthly in different cities | 11:08 |
| FourFire | > <nmz787_i> that channel was pretty boring the one or two times i popped in... i don't know why all you folks bring it up so much | 11:08 |
| chris_99 | xentrac, i don't afraid | 11:08 |
| FourFire | also fucking useless at helping pretty much anything... | 11:09 |
| xentrac | 16:40 < nmz787_i> as long as the plastic doesn't sag appreciably over the lifetime of your calibration/measurement | 11:09 |
| xentrac | I hadn't really appreciated how big of a problem creep is with plastics. but it's a huge problem! some plastics are almost immune, like PET | 11:09 |
| kanzure | "Chemical principles in tissue clearing and staining protocols for whole-body cell profiling" http://diyhpl.us/~bryan/papers2/bio/Chemical%20principles%20in%20tissue%20clearing%20and%20staining%20protocols%20for%20whole-body%20cell%20profiling%20-%202016.pdf | 11:10 |
| kanzure | this is a good review of tissue clearing stuff^ | 11:10 |
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| nmz787_i | xentrac: I really hadn't thought of it much recently at least, before I centrifuged that recently | 11:19 |
| kanzure | "Saturated reconstruction of a volume of neocortex" https://www.mcb.harvard.edu/mcb_files/media/editor_uploads/2015/07/PIIS0092867415008247.pdf | 11:23 |
| kanzure | this is also a good paper. | 11:23 |
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| kanzure | https://hackaday.io/project/12308-xatc-extreme-simple-automatic-tool-changer | 12:04 |
| kanzure | https://www.youtube.com/watch?v=sQgfjYIQCZs | 12:04 |
| kanzure | http://turingchurch.com/2016/06/21/paradiso-and-inferno-in-robin-hansons-the-age-of-em/ | 12:10 |
| kanzure | john smart is super spammy. wtf. | 12:15 |
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| nmz787_i | chris_99: looking at that kinematic mount STL file, it is obvious that the mirror/grating mount area is connected to the main part of the mount in the corner with a small bridge of plastic | 14:02 |
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| chris_99 | you mean connected to the metal part? | 14:03 |
| nmz787_i | chris_99: bottom right in this pic http://thingiverse-production-new.s3.amazonaws.com/renders/e1/32/d5/38/55/MM03_display_large.jpg | 14:04 |
| nmz787_i | between the inner square and the outer | 14:04 |
| nmz787_i | i guess it wouldn't be too hard to make something like this from metal or something else harder than plastic | 14:05 |
| chris_99 | mmm | 14:05 |
| nmz787_i | an aluminum can... maybe | 14:05 |
| nmz787_i | and a bar of steel for the screws | 14:07 |
| nmz787_i | (to hold them and attach to the aluminum) | 14:08 |
| chris_99 | i like the idea of using the metal frame they used for that plastic fitting | 14:09 |
| nmz787_i | yeah | 14:10 |
| nmz787_i | I think it need not be stiff, unless you're thinking about thermal expansion and stuff | 14:11 |
| nmz787_i | but it would be nice to be "less melty" than plastic | 14:11 |
| chris_99 | mm | 14:11 |
| nmz787_i | which metal is a few thousand degrees further from than plastics | 14:11 |
| nmz787_i | just started to print a lab jack | 14:13 |
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| chris_99 | lab jack? | 14:14 |
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| nmz787_i | chris_99: http://www.thingiverse.com/thing:925556/ | 14:50 |
| chris_99 | heh thats really cool | 14:51 |
| chris_99 | whatcha using it for | 14:51 |
| nmz787_i | no idea, but seems like a reasonable test of the printer | 14:54 |
| nmz787_i | and i have wanted one in the past | 14:54 |
| chris_99 | what 3d printer | 15:05 |
| chris_99 | do you have | 15:05 |
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| kanzure | .title | 15:05 |
| yoleaux | Platform Jack [Fully Assembled, No Supports] by Intentional3D - Thingiverse | 15:05 |
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| nmz787_i | it's an M3D that I borrowed from work | 15:11 |
| nmz787_i | supposed to be plug-n-play | 15:12 |
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| kanzure | "Whole-body and whole-organ clearing and imaging techniques with single-cell resolution: toward organism-level systems biology in mammals" http://www.qbic.riken.jp/syn-bio/publications/Cell%20Chemical%20Biology%20(2016).pdf | 15:14 |
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| kanzure | https://scholar.google.com/scholar?hl=en&q=Whole-Brain+Imaging+with+Single-Cell+Resolution+Using+Chemical+Cocktails+and+Computational+Analysis&btnG=&as_sdt=1%2C44&as_sdtp= | 15:16 |
| kanzure | "All 69 versions" that's the highest count i have seen on google scholar. wat? | 15:16 |
| kanzure | "Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis" (2014) https://www.researchgate.net/profile/Dimitri_Perrin/publication/261765493_Whole-Brain_Imaging_with_Single-Cell_Resolution_Using_Chemical_Cocktails_and_Computational_Analysis/links/00463539145f1ecdf0000000.pdf | 15:18 |
| kanzure | "Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging" (2015) http://www.qbic.riken.jp/syn-bio/publications/Susaki%20et%20al_NProt%202015.pdf | 15:21 |
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| kanzure | "Whole-body imaging with single-cell resolution by tissue decolorization" (2014) http://www.qbic.riken.jp/syn-bio/publications/Cell_20141106.pdf | 15:25 |
| kanzure | "Expression profile of 51 brain regions in adult mouse" http://brainstars.org/ | 15:30 |
| kanzure | hmm http://brainstars.org/ntnh/ | 15:31 |
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| kanzure | http://vibrism.neuroinf.jp/dev/201509/examples.html | 15:33 |
| kanzure | "Transcriptome tomography for creating comprehensive gene expression maps" https://www.youtube.com/watch?v=Td4rGRQIZuY | 15:33 |
| kanzure | "Transcriptome tomography for brain analysis in the web-accessible anatomical space" http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0045373 | 15:39 |
| kanzure | cool this is cheaper than the allen brain atlas method | 15:39 |
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| kanzure | "Zebrafish brain activation by pheromone prostaglandin F2α" https://www.youtube.com/watch?v=0-DTzMRLnO8 | 16:00 |
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| kanzure | "High-resolution fluorescence imaging of an entire fly brain" https://www.youtube.com/watch?v=eSoCLNAMy8U | 16:01 |
| kanzure | "A subset of neurons was labelled with GFP in this transgenic fly strain. The brain sample was cleared with SeeDB2 and high-resolution images of the entire brain were obtained with confocal microscopy." | 16:01 |
| kanzure | visualization of tooth formation in mouse embryo development https://www.youtube.com/watch?v=9k25YAwT0e4 | 16:05 |
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| kanzure | how about a tissue clearing technique where you use a gas or spray that liquifies a few nanometers of tissue at a time | 17:00 |
| kanzure | then after liquification occurs you wash off the layer | 17:00 |
| kanzure | presumably this would cause less destruction than a large blade which makes it hard to reconnect micro anatomy | 17:01 |
| kanzure | uh i guess an acid would work | 17:02 |
| kanzure | you could also lower the material into acid | 17:03 |
| kanzure | oh right, blades are used because they scan the sample after cutting, not before. bummer... | 17:04 |
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| kanzure | fenn: "Human blood metabolite timetable indicates internal body time" http://www.qbic.riken.jp/syn-bio/publications/PNAS(2012).pdf | 17:29 |
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| kanzure | why are they using blades and not lasers | 17:33 |
| kanzure | "A rapid optical clearing protocol using 2,2-thiodiethanol for microscopic observation of fixed mouse brain" http://journals.plos.org/plosone/article/asset?id=10.1371%2Fjournal.pone.0116280.PDF | 17:38 |
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| kanzure | "A versatile clearing agent for multi-modal brain imaging" http://www.nature.com/articles/srep09808.pdf | 17:43 |
| kanzure | "The most common approach, showed by the Allen Mouse Brain Atlas1 and the Mouse Brain Architecture Project2, is to slice the tissue into thin sections, then stain and image the sections with various techniques. However, precise cutting, mounting and imaging take a considerable amount of effort and time. Automated, high-throughput imaging methods based on serial sectioning have been recently developed either by embedding the sample in ... | 17:43 |
| kanzure | ... hard resin and slicing it in ultra-thin ribbons which are imaged just after slicing3,4 or by combining fixed tissue slicing with two-photon microscopy5. The major limitations of these techniques are the tissue deformation introduced by slicing and, intrinsically, the destruction of the sample." | 17:44 |
| kanzure | er what... then why not use lasers? | 17:44 |
| kanzure | "High refractive index organic solvents have been used for optical clearing of entire mouse brains7,8,9. Although these methods guarantee high transparency, protein fluorescence quenching and tissue shrinkage limit their applicability." | 17:45 |
| kanzure | [7] Dodt, H. U. et al. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat Methods 4, 331–336 (2007). | 17:45 |
| kanzure | [8] Becker, K., Jahrling, N., Saghafi, S., Weiler, R. & Dodt, H. U. Chemical clearing and dehydration of GFP expressing mouse brains. PLoS One 7, e33916 (2012). | 17:45 |
| kanzure | [9] | 17:45 |
| kanzure | [9] Renier, N. et al. iDISCO: A Simple, Rapid Method to Immunolabel Large Tissue Samples for Volume Imaging. Cell 159, 896–910 (2014). | 17:45 |
| kanzure | "Other approaches involving water-based optical clearing agents, such as Scale10, SeeDB11, ClearT12 and CUBIC13 were developed to allow improved preservation of fluorescence. Each of them, however, presents other non-negligible limitations such as long incubation times, structural alteration and incompatibility with immunostaining." | 17:45 |
| kanzure | i wonder if that means they are incompatible with aptamer labeling | 17:46 |
| kanzure | *also incompatible | 17:46 |
| kanzure | "... CLARITY14,15. This method transforms an intact tissue into a nanoporous, hydrogel-hybridized, lipid-free form. By removing membrane lipid bilayers, CLARITY allows high transparency, whole brain immunolabeling and structural and molecular preservation. This method, however, requires an expensive refractive index matching solution (FocusClearTM) whose composition is unknown due to patent protection, limiting its practical applicability" | 17:46 |
| kanzure | oh i did not know there ware patent concerns with that approach >:( | 17:46 |
| kanzure | focusclear tps://www.google.com/patents/US6472216 | 17:48 |
| kanzure | er.. | 17:48 |
| kanzure | focusclear https://www.google.com/patents/US6472216 | 17:48 |
| kanzure | SCALEVIEW-A2 http://www.google.com/patents/US20130045503 | 17:51 |
| kanzure | "benzyl-alcohol and benzyl-benzoate (BABB) solution described by Hans-Urich Dodt et al. (Nature Methods (2007) 4(4), 331 -336.)." i guess that was "Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain." | 17:52 |
| kanzure | "However, FocusClear solution shrinks biological samples and does not sufficiently clear turbidity of tissue area deeper than 0.5mm. SCALEVIEW-A2 solution requires a long incubation time for clearing, from weeks to months, and causes immense expansion in tissue volume, resulting in very fragile samples. In addition, SCALEVIEW-A2 solution cannot clear tiny tissues such as insect brains. BABB causes irreversible tissue shrinkage and, owing ... | 17:52 |
| kanzure | ... to its reliance on organic solvents, it quenches the fluorescent signal of immunohistochemistry, conventional lipophilic carbocyanine dyes and fluorescent tracers such as cholera toxin subunit B (CTB)." | 17:53 |
| kanzure | was from https://www.google.com/patents/WO2016004563A1 | 17:57 |
| kanzure | "The electrophoretic step of the CLARITY protocol causes the tissue to expand. We measured the linear deformation of the tissue caused by the clearing with TDE and with FocusClearTM. TDE, similarly to FocusClearTM, shrank the tissue back, producing a final tissue expansion of 16% (Fig. 3c). We processed with CLARITY and cleared with TDE the brain of an adult PV-cre-tdTomato mouse, in which parvabuminergic neurons were labeled with the ... | 17:59 |
| kanzure | ... tdTomato fluorescent protein." | 17:59 |
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| kanzure | "The direct incubation of TDE is not suitable for imaging entire organs. While in some approaches limitations due to insufficient clearing are overcome by slicing the sample in 1–1.5 mm thick slices21, here we pursued optimum transparency in the whole mouse brain by coupling TDE with the CLARITY technique. We found that TDE is a valid alternative to FocusClearTM as refractive index matching solution, considerably lowering the cost of ... | 18:07 |
| kanzure | ... every experiment and making large-volume, high-throughput imaging with LSM affordable." | 18:07 |
| kanzure | "Moreover, the unknown composition of FocusClearTM impaired any effort of the scientific community to further improve its clearing efficiency. For example, the refractive index variation achievable by different TDE/PBS percentages allows an ad hoc optimization of the clearing capability for different tissue types and permits integration of other compounds that can potentially improve the optical transparency of the selected specimen." | 18:07 |
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| kanzure | these guys suggest using multiple views of the same chunks of neural matter to assist with automatic segmentation, tracing and reconstruction http://arxiv.org/pdf/1511.01168.pdf | 18:15 |
| kanzure | https://github.com/paolo-f/bcfind "Brain cell finder is a tool for fully automated localization of soma in 3D mouse brain images acquired by confocal light sheet microscopy" | 18:16 |
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| kanzure | "Concrete problems in AI safety" https://arxiv.org/pdf/1606.06565v1.pdf | 18:35 |
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| kanzure | "Towards an integration of deep learning and neuroscience" http://biorxiv.org/content/biorxiv/early/2016/06/13/058545.full.pdf | 18:48 |
| kanzure | above seems to be from marblestone | 18:49 |
| kanzure | who is "neo marblestone" | 18:51 |
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| kanzure | cc maaku | 19:20 |
| kanzure | hmm church and marblestone with hamalainen kemmish and the andregg brothers in 2013 re: dna stretching on a water droplet surface http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069058 | 19:26 |
| kanzure | i was not aware that halcyon molecular got the idea from those guys | 19:26 |
| kanzure | molecular ticker tape stuff "Recording neural activities onto DNA" https://projectreporter.nih.gov/project_description.cfm?projectnumber=1R01MH103910-01 | 19:32 |
| streety | I've been doing some work with clarity and perfusion assisted clearing. What is TDE? | 19:32 |
| kanzure | TDE seems to be an alternative to FocusFlow | 19:32 |
| streety | another issue with the organic solvent approaches is that they are incompatible with many objectives | 19:32 |
| kanzure | with a known composition and no patents | 19:32 |
| streety | where were you pulling those quotes from? | 19:33 |
| kanzure | what do you mean, how can you not solve all your problems by dissolving organic matter in acids | 19:33 |
| kanzure | 1) my butt 2) usually the previous link | 19:33 |
| kanzure | and some of the quotes after the SCALEVIEW-A2 link were from patents, but then they returned to being quotes from the "A versatile clearing agent for multi-modal brain imaging" paper http://www.nature.com/articles/srep09808.pdf | 19:34 |
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| kanzure | it seems that CLARITY originally required FocusFlow or something | 19:34 |
| streety | thanks | 19:36 |
| kanzure | whatcha up to | 19:36 |
| streety | I've also seen 70% sorbitol suggested | 19:37 |
| streety | trying to image kidney tissue samples | 19:37 |
| streety | Would be nice to handle an entire mouse kidney, hence perfusion clearing, but looking like that will be beyond our capabilities for a while | 19:38 |
| kanzure | fahy probably has many hints for you if you spam him by emai | 19:38 |
| kanzure | 19:38 | |
| kanzure | because of his kidney vitrification work | 19:39 |
| streety | I haven't seen that | 19:39 |
| kanzure | https://en.wikipedia.org/wiki/Greg_Fahy | 19:40 |
| streety | first article I found is as old as I am | 19:40 |
| kanzure | "Fahy is the world's foremost expert in organ cryopreservation by vitrification.[1][2][3] Fahy introduced the modern successful approach to vitrification for cryopreservation in cryobiology[4][5][6][7][8][9][10][11] and he is widely credited, along with William F. Rall, for introducing vitrification into the field of reproductive biology.[7][12] In the summer of 2005, where he was a keynote speaker at the annual Society for Cryobiology ... | 19:40 |
| kanzure | ... meeting, Fahy announced that Twenty-First Century Medicine had successfully cryopreserved a rabbit kidney at -130 °C by vitrification and transplanted it into a rabbit after rewarming, with subsequent long-term life support by the vitrified-rewarmed kidney as the sole kidney." | 19:40 |
| kanzure | he is quite friendly to the alcor and cryonics and transhumanism communities | 19:41 |
| kanzure | in fact, the guy who did the pokemon yellow total control hack was once an employee working for fahy | 19:42 |
| streety | I've got some reading to do. Might actually be some relevance to an entirely separate project I'm working on with the liver work | 19:43 |
| streety | I really need to start writing up some of my more complete projects and moving on | 19:44 |
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| kanzure | "neurithmic systems llc" https://www.iarpa.gov/images/files/programs/MICrONS/Neurithmic_Systems.pdf | 20:45 |
| kanzure | "Machine intelligence from cortical networks: proposers' day abstracts" https://www.iarpa.gov/images/files/programs/MICrONS/MICrONS_abstracts.pdf | 20:45 |
| kanzure | "This device, now resident in my laboratory, uses 61 beams to image at speed approaching 1 billion pixels per second at 4nm resolution using secondary electrons. These tools may be useful for the acquisition of large brain samples." | 20:47 |
| kanzure | page 13 "New tools for high-throughput electron microscopy of brain tissue" | 20:49 |
| kanzure | page 25 "%LRORJLFDOO\UHDOLVWLFFLUFXLWU\IURPKLSSRFDPSDOQHXURQSURSHUWLHV | 20:50 |
| kanzure | what.. | 20:50 |
| kanzure | "Biologically realistic circuitry from hippocampal neuron properties" | 20:51 |
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| kanzure | lamdal.com "machine learning contractors" well at least someone is occupying that niche | 20:53 |
| Regex__ | kanzure: I've seen you post a lot of papers on brains. Are you trying to gather information for something in particular? | 20:54 |
| kanzure | "Conneconomics: The Economics of Dense, Large-Scale, High-Resolution Neural Connectomics" http://biorxiv.org/content/early/2014/04/20/001214 | 20:55 |
| kanzure | "Due to advances in parallel-beam instrumentation, whole mouse brain electron microscopic image acquisition could cost less than $100 million, with total costs presently limited by image analysis to trace axons through large image stacks. Optical microscopy at 50 to 100 nm isotropic resolution could potentially read combinatorially multiplexed molecular information from individual synapses, which could indicate the identifies of the ... | 20:55 |
| kanzure | ... pre-synaptic and post-synaptic cells without relying on axon tracing. An optical approach to whole mouse brain connectomics may be achievable for less than $10 million and could be enabled by emerging technologies to sequence nucleic acids in-situ in fixed tissue via fluorescent microscopy. Novel strategies relying on bulk DNA sequencing, which would extract the connectome without direct imaging of the tissue, could produce a whole ... | 20:55 |
| kanzure | ... mouse brain connectome for $100k to $1 million or a mouse cortical connectome for $10k to $100k. Anticipated further reductions in the cost of DNA sequencing could lead to a $1000 mouse cortical connectome." | 20:55 |
| kanzure | Regex__: i hope you die in a fire | 20:55 |
| * kanzure sleeps | 20:55 | |
| kanzure | wait one more: "Rosetta Brains: A Strategy for Molecularly-Annotated Connectomics" http://arxiv.org/abs/1404.5103 | 20:56 |
| kanzure | "We propose a neural connectomics strategy called Fluorescent In-Situ Sequencing of Barcoded Individual Neuronal Connections (FISSEQ-BOINC), leveraging fluorescent in situ nucleic acid sequencing in fixed tissue (FISSEQ). FISSEQ-BOINC exhibits different properties from BOINC, which relies on bulk nucleic acid sequencing. FISSEQ-BOINC could become a scalable approach for mapping whole-mammalian-brain connectomes with rich molecular ... | 20:56 |
| kanzure | ... annotations." | 20:56 |
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