| --- Log opened Sat Mar 26 00:00:10 2016 | ||
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| kanzure | "The role of photonics in energy" http://photonicsforenergy.spiedigitallibrary.org/article.aspx?articleid=2463108 | 06:48 |
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| kanzure | "Neurokernel: An Open Source Platform for Emulating the Fruit Fly Brain" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4709234/ | 06:54 |
| kanzure | figure 1 "Modular structure of the fruit fly brain" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4709234/bin/pone.0146581.g001.jpg | 06:54 |
| kanzure | various RFCs http://neurokernel.github.io/docs.html | 06:57 |
| kanzure | https://github.com/neurokernel/neurokernel | 07:01 |
| kanzure | https://github.com/neurokernel/antennal_lobe/blob/master/notebooks/olfaction.ipynb | 07:05 |
| kanzure | .title https://www.youtube.com/watch?v=3hPsmZXpylM | 07:06 |
| yoleaux | The Retina as a Parallel Information Pre-Processor - YouTube | 07:06 |
| kanzure | that fig1 above link is bad, use http://diyhpl.us/~bryan/papers2/neuro/Neurokernel:%20An%20open%20source%20platform%20for%20emulating%20the%20fruit%20fly%20brain%20-%202016.pdf.fig1.jpg | 07:11 |
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| kanzure | https://lists.columbia.edu/mailman/listinfo/neurokernel-dev | 07:12 |
| kanzure | .title https://www.youtube.com/watch?v=pSokol2AkWg | 07:12 |
| yoleaux | Digital Worms and Flies: OpenWorm meets Neurokernel - YouTube | 07:12 |
| kanzure | "‘Connectomics-based analysis of information flow in the Drosophila brain" http://diyhpl.us/~bryan/papers2/neuro/Connectomics-based%20analysis%20of%20information%20flow%20in%20the%20Drosophila%20brain%20-%202015.pdf | 07:16 |
| kanzure | http://www.flycircuit.tw/ | 07:16 |
| kanzure | http://www.flycircuit.tw/flycircuit_images/wiringdiagramFemale/female.jpg | 07:17 |
| kanzure | http://bigneuron.org/ seems to be broken :| | 07:25 |
| kanzure | "Neuron anatomy structure reconstruction based on a sliding filter" http://diyhpl.us/~bryan/papers2/neuro/Neuron%20anatomy%20structure%20reconstruction%20based%20on%20a%20sliding%20filter%20-%202015.pdf | 07:27 |
| kanzure | http://diademchallenge.org/ | 07:32 |
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| kanzure | (music) https://www.youtube.com/watch?v=ZXcQv9Sj3JM&t=1m50s | 07:48 |
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| fenn | .wik diadem | 10:12 |
| yoleaux | "A diadem is a type of crown, specifically an ornamental headband worn by monarchs and others as a badge of royalty. The word derives from the Greek διάδημα diádēma, "band" or "fillet", from διαδέω diadéō, "I bind round", or "I fasten"." — https://en.wikipedia.org/wiki/Diadem | 10:12 |
| fenn | the "challenge" is automatic neuron tracing and reconstruction (i thought this already existed? i saw it at 3scan for sure) | 10:14 |
| fenn | oh it was in 2010 | 10:14 |
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| kanzure | fenn: ehh i don't think either of us ever saw 3scan's actual method, just some output. | 11:42 |
| kanzure | which doesn't tell us how accurate the method was | 11:43 |
| kanzure | also, what we saw was visual reconstruction (i think).... which might have used manual tracing as input. | 11:43 |
| kanzure | diadem was 2010 but bigneuron is 2015-now | 11:43 |
| kanzure | https://github.com/bigneuron | 11:56 |
| kanzure | reconstruction results https://docs.google.com/spreadsheets/d/1k0hA5oByPLbKLWqdQlvQiEAJNFTQCSSgjKYFCxEdY6s/edit#gid=102202457 | 11:57 |
| kanzure | https://github.com/BigNeuron/BigNeuron-Wiki/wiki/Neuron-Reconstruction-Algorithms | 11:58 |
| kanzure | "High-accuracy neurite reconstruction for high-throughput neuroanatomy" (2011) http://www.nature.com/neuro/journal/v14/n8/full/nn.2868.html | 11:58 |
| kanzure | some image data sets https://www.dropbox.com/sh/c7tttjv0vicgdo5/AADma_T9New3uGcIA6ofEpWZa?dl=0 | 12:02 |
| kanzure | "The total size of these data is about 19GB (of 79 neurons)." what? | 12:04 |
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| holz_ | how do i put the internet in my brain | 14:07 |
| yashgaroth | do you have a corkscrew handy | 14:14 |
| kanzure | i only have a paperclip and three rubber bands. please advise. | 14:15 |
| yashgaroth | fashion a crude FM transmitter | 14:15 |
| holz_ | i have an old microwave | 14:22 |
| yashgaroth | yeah that'll work, but you'll be capped at 256k | 14:25 |
| jrayhawk | the internet is a worldwide interconnected network of computers. you have two options: make the world small enough to fit in your brain, or make your brain large enough to encompass the world. | 14:25 |
| jrayhawk | my recommendation: cultivate a variety of brain cancers in the hope of becoming the next HeLa | 14:27 |
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| kanzure | that's a good plan because it has a chance of working | 14:36 |
| FourFire | whoo back | 14:57 |
| FourFire | just gave in to the overlords, have windows 10 and an SSD RAID0 now | 14:58 |
| FourFire | jrayhawk, but surely, you could merely have your brain digitized and have parts running in clusters worldwide | 14:59 |
| FourFire | then your brain is the internet. | 14:59 |
| FourFire | latency will be tehsuck, but probably not substantially worse than grey meat | 14:59 |
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| jrayhawk | you're right, i suppose postmodernism is a better approach | 15:05 |
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| fenn | kanzure: no i saw matt goodman writing image processing code to remove camera artifacts because it was messing with the (presumably pre-existing) segmentation code | 16:01 |
| fenn | this would have been a lot of tracing http://www.3scan.com/gallery/ | 16:04 |
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| maaku | jrayhawk: you are in fact already one neuron in the global brain | 16:14 |
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| kanzure | i wonder if most of those tracing algorithms are compatible with multiple rounds of antibody staining and washing per slice. | 16:20 |
| Aurelius_Laptop | kanzure : while I'm continuing my CS education, I've decided while I job hunt for my next job to focus on marginal advantage, so this means data science and machine learning it seems (focused on business intelligence/analysis problems) | 16:21 |
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| -!- Topic for ##hplusroadmap: biohacking, nootropics, transhumanism, open hardware | sponsored by lobsters everywhere, banned by the Federal Death Administration (5 times) | this channel is LOGGED: http://gnusha.org/logs | http://diyhpl.us/wiki | "ray kurzweil is a pessimist" - george church | 17:19 | |
| -!- Topic set by kanzure [~kanzure@unaffiliated/kanzure] [Wed May 20 12:46:25 2015] | 17:19 | |
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| kanzure | http://vaa3d.org/ | 18:35 |
| kanzure | .title https://www.youtube.com/watch?v=ycWVTVQtUFg | 18:36 |
| yoleaux | v3d fly neuron trace disp - YouTube | 18:36 |
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| kanzure | .title https://www.youtube.com/watch?v=-Y8kDURdJr8 | 18:51 |
| yoleaux | fly brain compartment atlas 090401 - YouTube | 18:51 |
| kanzure | why did someone write yet another scientific visualization visualizer | 18:52 |
| kanzure | https://github.com/Vaa3D/vaa3d_tools/blob/master/released_plugins/v3d_plugins/global_neuron_feature/compute.cpp | 18:54 |
| kanzure | https://github.com/Vaa3D/vaa3d_tools/blob/master/released_plugins/v3d_plugins/neuron_stitch/neuron_stitch_func.cpp | 18:57 |
| kanzure | these seem to be the "original" algorithms from diadem? https://github.com/Vaa3D/vaa3d_tools/tree/master/bigneuron_ported/neuronAssembler | 19:03 |
| kanzure | like neutube: https://github.com/Vaa3D/vaa3d_tools/blob/master/bigneuron_ported/neuronAssembler/neutube/NeuronAssembler_NeuTube_plugin.cpp | 19:04 |
| kanzure | i like how there are no unit tests for any of this shit | 19:05 |
| kanzure | oh.... https://github.com/janelia-flyem/NeuTu/tree/public/neurolabi/c | 19:07 |
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| kanzure | https://svn.janelia.org/penglab/projects/vaa3d_tools/hackathon/zhi/ | 19:12 |
| kanzure | janelia is a weird science thing | 19:17 |
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| maaku | http://vncroulette.com/ | 20:44 |
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