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| ||0_-_0|| | paperbot http://www.nature.com/nsmb/journal/v21/n6/full/nsmb.2820.html?WT.ec_id=NSMB-201406 | 00:02 |
|---|---|---|
| paperbot | http://libgen.org/scimag/get.php?doi=10.1038%2Fnsmb.2820 | 00:02 |
| ||0_-_0|| | paperbot http://www.nature.com/nmeth/journal/v11/n6/full/nmeth.2934.html?WT.ec_id=NMETH-201406 | 00:04 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1038%2Fnmeth.2934 | 00:04 |
| ||0_-_0|| | paperbot <3 <3 <3 | 00:04 |
| gradstudentbot | Okay, someone really needs to do the lab dishes. | 00:04 |
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| nmz787 | that zeiss is pretty average for a multi-light source and trinocular (possibly fluorescense) scope | 00:35 |
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| seba- | [14:02] <horsefiend> so i went home, alone, with my wine and maaged to get meth anyway, I used 200mg of it IV and then threw up blood... so i am thinking also that perhaps i am sufffering from something which IV aspirin may be favourable for... | 05:06 |
| seba- | lol | 05:06 |
| nshlol | i don't always practice adultery, but when i do, it's with my bloodstream | 05:07 |
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| seba- | full quote: http://pastebin.com/5NhbP39S | 05:14 |
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| catern | lol | 06:01 |
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| nmz787_i | I seem to be experiencing a imported function fails to call in exception where the interpreter crashes/closes | 10:01 |
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| kanzure | i am not sure if grammar | 10:06 |
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| kanzure | are you talking about an ImportError? | 10:07 |
| dingo | an exception occured while handling an exception | 10:07 |
| kanzure | https://github.com/docker/libswarm | 10:07 |
| kanzure | "Simulate your entire service topology in a single process" | 10:07 |
| kanzure | an open source embedded microprocessor core https://github.com/atgreen/moxiedev http://www.moxielogic.org/wiki http://www.moxielogic.org/blog | 10:13 |
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| nmz787_i | hmm idk | 10:16 |
| nmz787_i | i'm not reproducing an error in demo | 10:16 |
| archels_ | .title http://www.nytimes.com/2014/06/10/health/a-chilling-medical-trial.html | 10:21 |
| yoleaux | archels_: Sorry: that command is a web-service, but its response was too long. | 10:21 |
| archels_ | nothing new, but good that this is going mainstream | 10:21 |
| archels_ | probably also good news for the cryo crowd | 10:21 |
| archels_ | (bearing in mind that Alcor whistleblower blog or whatever it was) | 10:22 |
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| kanzure | gene_hacker: has matt encountered or made a graph grammar for optical train design? | 10:36 |
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| gene_hacker | no | 10:46 |
| gene_hacker | there are expert systems that will beat almost any human at optical system design though | 10:46 |
| gene_hacker | why are you making all your optics yourself btw? | 10:46 |
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| kanzure | gene_hacker: because having a model is a good thing, it lets you simulate before building | 10:56 |
| gene_hacker | why not use a microscope whose properties you know? | 10:56 |
| kanzure | but you don't know- nobody has detailed data about "hey, we're projecting LEDs through microscopes and here's how the images turn out" | 10:59 |
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| kanzure | .title https://www.youtube.com/watch?v=Og9M7xIhW00 | 11:33 |
| yoleaux | Virtual Atomic Force Microscope using Interactive MD with LAMMPS and VMD | 11:33 |
| kanzure | cc eudoxia | 11:33 |
| kanzure | gene_hacker: however, your idea is probably better.. looks like nobody has done an accurate simulation of a microscope ever. wtf? | 11:35 |
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| eudoxia | kanzure: you know me too well | 11:43 |
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| kanzure | win 3 | 12:03 |
| kanzure | lkdfjdsafja; | 12:03 |
| gradstudentbot | This laproscopic camera is so easy to use. | 12:05 |
| kanzure | .title http://hydracarina.org/910 | 12:33 |
| yoleaux | Howto mount an infinity corrected microscope objective on a camera | 12:33 |
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| kanzure | .title http://www.krebsmicro.com/obj_bellows/index.html | 12:34 |
| yoleaux | kanzure: Sorry, that command (.title) crashed. | 12:34 |
| kanzure | "Microscope Objectives on Camera Bellows" | 12:34 |
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| nmz787_i | hmm | 13:12 |
| nmz787_i | cad but no prices http://www.velmex.com/bislide/motor_bislide.html | 13:12 |
| nmz787_i | kanzure: i've come across that hydracarina link before, is a good ref, good reminder of it! | 13:13 |
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| nmz787_i | omg finally figured out the hanging pipe crap | 13:16 |
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| nmz787_i | if you use popen with pythonw.exe, you have to provide a fd for the stdin arg to popen... also in this case, you can't try doing sys.__stderr__.write(string) because it will cause an error (which you won't be able to see unless you're redirecting stderr in this process to a GUI textbox) | 13:18 |
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| -!- Topic for ##hplusroadmap: biohacking, nootropics, transhumanism, open hardware | sponsored by george church and the NRA, banned by the Federal Death Administration (4 times) | this channel is LOGGED: http://gnusha.org/logs | http://diyhpl.us/wiki | not intentionally unrepeatable | 13:32 | |
| -!- Topic set by kanzure [~kanzure@131.252.130.248] [Fri Jun 6 17:48:33 2014] | 13:32 | |
| [Users ##hplusroadmap] | 13:32 | |
| [ Adifex ] [ devrandom ] [ JayDugger ] [ rk[1] ] | 13:32 | |
| [ andytoshi ] [ dingo ] [ jrayhawk_ ] [ ruphos ] | 13:32 | |
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| [ catern ] [ gene_hacker ] [ nmz787_i ] [ ThomasEgi ] | 13:32 | |
| [ chris_99 ] [ gnusha ] [ paperbot ] [ Twey ] | 13:32 | |
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| -!- Channel ##hplusroadmap created Thu Feb 25 23:40:30 2010 | 13:32 | |
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| dingo | good on you | 13:33 |
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| justanotheruser | welcome back to the mainnet | 13:33 |
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| kanzure | did i die | 13:49 |
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| archels_ | paperbot: http://www.nrcresearchpress.com/doi/pdf/10.1139/y94-080 | 13:57 |
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| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/358920edfa35f8bdfecf8f41d0903c5e.txt | 13:57 |
| archels_ | yeah, welcome to hell. there's no free paper access here either | 13:58 |
| justanotheruser | archels_: please hold | 14:02 |
| justanotheruser | hmm, I'm signed in for http://www.ncbi.nlm.nih.gov/pubmed/7954086, but I can't find a download link | 14:05 |
| archels_ | well... it's in a 1994 issue of the Canadian Journal of Physiology and Pharmacology | 14:06 |
| archels_ | I guess it was a long shot | 14:06 |
| archels_ | thanks for trying though | 14:06 |
| justanotheruser | yeah, sorry I couldn't get it | 14:06 |
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| delinquentme | paperbot, http://www.nature.com/ncomms/2014/140610/ncomms5082/full/ncomms5082.html | 14:20 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1038%2Fncomms5082 | 14:20 |
| delinquentme | kanzure, paper isn't actually fetching novel papers right now right? | 14:22 |
| delinquentme | "novel papers" = papers which aren't already on libgen | 14:22 |
| kanzure | if it's on libgen, i think it skips it | 14:23 |
| gradstudentbot | My study reveals that people are awesome at memorizing insecure passwords. | 14:24 |
| delinquentme | kk, so that paper isn't on libgen and Mr. Paper failed to get it from nature | 14:24 |
| delinquentme | problem? | 14:24 |
| kanzure | yes it most likely doesn't have the pdf | 14:25 |
| kanzure | .title http://www.sciencedirect.com/science/article/pii/S0378517307010113 | 14:25 |
| yoleaux | Size analysis of submicron particles by laser diffractometry—90% of the published measurements are false | 14:25 |
| kanzure | (haha, people can't use microscopes) | 14:25 |
| kanzure | or diffractometers | 14:25 |
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| delinquentme | kanzure, libgen clearly does not. So paperbot isn't fetching them via shibboleth ? | 14:32 |
| delinquentme | " If libgen doesn't have the paper , why isn't paperbot fetching it an uploading it to libgen ? " | 14:32 |
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| kanzure | paperbot does not have access to shibboleth | 14:34 |
| kanzure | as far as i know | 14:34 |
| kanzure | did someone add that? | 14:34 |
| delinquentme | I thought that was how it was downloading papers | 14:35 |
| delinquentme | I thought he downloaded papers from nature? | 14:36 |
| kanzure | shibboleth is not nature | 14:36 |
| delinquentme | ... no shit | 14:36 |
| kanzure | so again, paperbot does not have access to shibboleth | 14:37 |
| delinquentme | Why isn't it downloading the papers if its not on libgen? | 14:38 |
| kanzure | probably because it doesn't have access, like any other time it can't download something | 14:38 |
| delinquentme | is this a new thing that has gone wrong ? or has it not had access to nature? | 14:39 |
| kanzure | nature.com is not a single access system | 14:39 |
| kanzure | nobody has /full/ access | 14:39 |
| delinquentme | so paperbot has some access to nature but not this journal | 14:45 |
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| delinquentme | ? | 14:45 |
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| kanzure | who knows- sometimes the restrictions are per paper, per journal, per "year published", per "year accepted", per "number of diagrams"... | 14:46 |
| delinquentme | and this is just per whoevers access we're using at the time | 14:49 |
| delinquentme | you and nmz are jumping into the lasercutter game again? | 14:50 |
| delinquentme | this is dumb that I cant get this paper instantly =/ | 14:50 |
| kanzure | i forget if it's a cutter or not | 14:51 |
| kanzure | it points light at things, does that help? | 14:51 |
| delinquentme | ablation ? | 14:51 |
| kanzure | what is it called when you point it at a photoresist.. absorption? | 14:51 |
| delinquentme | I want bioreactors which keep cells alive and make blood | 14:51 |
| delinquentme | yeah probs | 14:52 |
| delinquentme | This whole ' young blood ' just seems a really convincing abstraction for youthfulness in my mind. | 14:52 |
| gradstudentbot | I am sponsored by Thermo Fisher. | 14:54 |
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| heath | what do you call someone who's name is an emoticon? pipe pipe zero underscore dash underscore zero pipe pipe? ppzuduzpp? | 15:05 |
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| FourFire | heath, it's not a verbal name | 15:18 |
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| kanzure | oh yeah, maybe i should convert mcad to python-brlcad https://github.com/elmom/MCAD | 15:48 |
| kanzure | dpk: i think the "fix zotero's translators-scrapers to make them not require gecko or zotero" project is the one i'm most interested in | 15:59 |
| kanzure | dpk: so that i can stop using zotero, and also get the benefit of zotero's community focusing on scrapers for me | 16:00 |
| dpk | okay, that was more or less my plan anyway | 16:00 |
| kanzure | unfortunately this means that it can't be pure python, which is a shame.. | 16:00 |
| dpk | i did some preliminary investigation and discovered that JavaScript is a load of cocks, but otherwise the plan is good | 16:01 |
| kanzure | have you written js things before? | 16:01 |
| dpk | just needs a good embeddable-into-both-paperbot-and-zotero scraping framework behind it | 16:01 |
| dpk | yeah | 16:01 |
| kanzure | i would have expected you to know already that js sucks? | 16:01 |
| dpk | my consistent experience has been that JavaScript is a load of cocks, indeed | 16:02 |
| kanzure | well, paperbot can be thrown away and replaced with a js version | 16:02 |
| kanzure | the actual irc bot integration is not important to me.. i mean that is simple to hack up later. | 16:02 |
| dpk | but it's always good to rediscover things in new ways, to help improve understanding of them | 16:02 |
| dpk | in this case i came to a new way of understanding the load-of-cocksiness of JavaScript | 16:02 |
| kanzure | i haven't thought strongly about how i would do the zotero integration | 16:03 |
| kanzure | one way is that you could have commonjs stuff, and just require() a vendorized dependency of scrapers | 16:03 |
| kanzure | another way is that you could have a tool that takes the nodejs/browserify-compatible scrapers and dumps them into a format that zotero is capable of using | 16:04 |
| dpk | well i assume that if it runs in the browser, it can run in Zotero? | 16:04 |
| kanzure | well, no, zotero itself has its own api | 16:04 |
| dpk | in that case i'd be inclined to just browserify the whole thing | 16:04 |
| dpk | oh, right | 16:04 |
| kanzure | https://github.com/zotero/translators | 16:04 |
| dpk | oh, that one | 16:04 |
| dpk | i assumed it just ran on top of the browser's JS libraries | 16:05 |
| kanzure | nah it uses this global called Zotero | 16:05 |
| kanzure | https://github.com/zotero/translators/blob/master/American%20Institute%20of%20Aeronautics%20and%20Astronautics.js | 16:05 |
| kanzure | and it has these doWeb, detectWeb, scrape functions | 16:05 |
| dpk | okay, hmm | 16:06 |
| dpk | i think the first option is probably the better one then | 16:07 |
| dpk | or specify some basic HTTP scraping interface which they can provide a shim for | 16:07 |
| gradstudentbot | The smell of e.coli is so very rewarding. | 16:07 |
| dpk | where does gradstudentbot get these things from? heh | 16:07 |
| gradstudentbot | Argh, what do you mean you don't accept LaTeX submissions?? | 16:07 |
| dpk | is it just a database of lines to regurgitate a la fortune? | 16:08 |
| kanzure | yep, but he's surprisingly sentient | 16:08 |
| kanzure | so, they are not going to be willing to send their scraping work over http to some other server | 16:09 |
| kanzure | the scrapers/parsers should definitely be local | 16:09 |
| dpk | right, i'm not proposing that | 16:09 |
| dpk | i mean 'interface' in the sense of 'just write a class/module that has these methods' | 16:09 |
| kanzure | zotero/translation-server has an http server where you submit a json request and get back a json response | 16:10 |
| kanzure | the json response is based on the bibliographic data that the scraper returns | 16:10 |
| dpk | ... i see | 16:10 |
| kanzure | i had to hack it to get it to return the pdf url to paperbot, | 16:11 |
| gradstudentbot | Protip: the lab's attic hasn't been used since 1966. Pretty nice. | 16:11 |
| kanzure | https://github.com/kanzure/translation-server/commit/4d35648672c1ff2d2b6c61308ac7fcb684d63448 | 16:11 |
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| kanzure | https://github.com/kanzure/translation-server/blob/4d35648672c1ff2d2b6c61308ac7fcb684d63448/src/server_translation.js | 16:12 |
| kanzure | such a terrible system | 16:12 |
| kanzure | oh huh i didn't know about /refresh | 16:12 |
| dpk | the new library of scrapers would be embedded in translation-server, then? | 16:14 |
| kanzure | translation-server accesses the zotero translators through some environment variable containing a path | 16:15 |
| kanzure | heh | 16:15 |
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| kanzure | translation-server is totally irrelevant to me, i'm only using it because it's a quick way to be using gecko/xulrunner | 16:16 |
| kanzure | to be using xulrunner/zotero, i mean | 16:16 |
| chris_99 | anyone know can freecad/brlcad work with autocad files | 16:16 |
| dpk | i see | 16:16 |
| kanzure | it actually doesn't work for all of the zotero translators because some of the translators use frames and link navigation, which xulrunner doesn't support(??) according to simonster | 16:16 |
| kanzure | so some of the translators are failing | 16:16 |
| kanzure | chris_99: dxf | 16:16 |
| kanzure | chris_99: .step .iges are also exportable from autocad, which both freecad (opencascade) and brlcad are able to work with | 16:17 |
| chris_99 | aha neat | 16:17 |
| kanzure | dpk, so maybe you're right, standard interface, every zotero translator is just a thin wrapper that someone writes, calls the appropriate sanely-architected scraper | 16:19 |
| kanzure | dpk: but then those sanely-architected scrapers need to be packaged into zotero and available | 16:19 |
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| * dpk nkds | 16:19 | |
| dpk | *nods | 16:19 |
| kanzure | i wonder how js imports work in xul-related js, is it just require() | 16:20 |
| kanzure | https://github.com/firebug/firebug/blob/master/extension/modules/require.js | 16:21 |
| kanzure | https://github.com/firebug/firebug/blob/master/extension/modules/mini-require.js | 16:21 |
| kanzure | but that's requirejs gah | 16:21 |
| dpk | yeah, fuck requirejs | 16:22 |
| dpk | not doing that | 16:22 |
| dpk | well, maybe if there's literally no other option | 16:23 |
| kanzure | looks like require() is baked in these days | 16:24 |
| kanzure | ok, so it can be a git submodule in zotero/translators.git that references something else that assembles/caches/compiles/dumps the saner scrapers | 16:25 |
| kanzure | each translator in zotero/translators.git can just be a thin wrapper that uses require("./sanestuff/whatever.js") and calls those functions | 16:25 |
| dpk | yeah | 16:25 |
| kanzure | and those would probably be browserify bundle outputs | 16:28 |
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| kanzure | dpk: this was my streaming parser attempt https://github.com/kanzure/papermonk-downloader-plosone | 16:36 |
| dpk | hmm, i didn't see that, only the main papermonk repo | 16:37 |
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| kanzure | i think i have my pipes fucked up =) | 16:38 |
| dpk | i am going to sleep now. i will investigate the Zotero/node thing tomorrow morning and hopefully have a solid plan by the time you show up in (my time) the afternoon | 16:38 |
| kanzure | okie dokie | 16:39 |
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| delinquentme | kanzure, where was it that you said had solid internet infrastructure, high quality research + cheap living? | 16:44 |
| delinquentme | china right? | 16:44 |
| delinquentme | ever thought about living there? | 16:44 |
| kanzure | i'm not opposed to it, but i never put a lot of thought into it | 16:45 |
| delinquentme | I really want to find applications at the junction of simple manufactured objects + programming + electronics and version control | 16:46 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=9bd2883f Bryan Bishop: move diybio faq file >> http://diyhpl.us/diyhpluswiki/diybio/faq/software/ | 16:52 |
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| heath | delinquentme: ukraine? | 17:27 |
| delinquentme | heath, Im guessing the political stuff doesnt help | 17:28 |
| heath | far cheaper living and internet infrastructure than what i have | 17:28 |
| kanzure | oh yeah, for larger objects you can just blast sound at them to separate them: http://www.elmat.lth.se/fileadmin/user_upload/Publications/04_Analyst_Petersson.pdf | 17:42 |
| kanzure | ugh but did they have to call it "acoustophoresis"? | 17:44 |
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| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=f1b63a7b Bryan Bishop: various microfluidic designs for diybio >> http://diyhpl.us/diyhpluswiki/diybio/microfluidics/ | 17:55 |
| kanzure | yashgaroth: http://diyhpl.us/wiki/diybio/microfluidics/ | 17:57 |
| kanzure | yashgaroth: what obvious and important equipment am i forgetting about? | 17:57 |
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| yashgaroth | lemme eat dinner first | 18:13 |
| yashgaroth | ok well I'm not sure what techniques can be used in microfluidics, but let's see...you surely will not be able to pack traditional chromatography resins microfluidically, but monoliths would mostly solve that | 18:29 |
| yashgaroth | how big are the channels typically? | 18:29 |
| kanzure | let's say we're aiming for between 10-100 microns (inclusive) | 18:30 |
| kanzure | and the other dimension can be up to multiple millimeters or centimeters if really necessary | 18:30 |
| yashgaroth | yeah you'd be fitting in traditional beads in single file with those dimensions | 18:31 |
| kanzure | i think you can easily purchase microbeads 1-5 micron diameter | 18:31 |
| seba- | lol | 18:31 |
| kanzure | or make them | 18:31 |
| kanzure | emulsions + curing or something | 18:31 |
| kanzure | chromatography columns require high pressure that i'm not sure would be compatible with these chips. not sure. | 18:32 |
| yashgaroth | ehhhh high pressure chromatography does, but it depends what you want to do | 18:32 |
| yashgaroth | if it's just 'stick DNA to this under condition X and elute under condition Y', you don't need pressure | 18:33 |
| kanzure | antibody purification would be nice | 18:33 |
| gradstudentbot | I think my PI hates me. | 18:33 |
| yashgaroth | purification of antibody, or by antibody? | 18:33 |
| kanzure | of antibody | 18:33 |
| yashgaroth | oh yeah you can do that; high pressure stuff is only for separating out things with a high resolution...purification you don't need pressure | 18:34 |
| yashgaroth | stick recombinant Protein A to/in your channel somehow, run crude stuff over it, wash, knock it off with another buffer | 18:35 |
| delinquentme | yashgaroth, do you have chromatography columns for sale OOC? | 18:35 |
| kanzure | could probably get that protein stuck to microbeads/spheres if not the channel | 18:35 |
| yashgaroth | I may, what you lookin' for bruv? | 18:35 |
| delinquentme | Or have the capability to get heparin sepharose 4B at price reductions ? | 18:35 |
| delinquentme | yashgaroth, a 16/20 GE column | 18:36 |
| yashgaroth | heh I used to have a bunch of heparin sepharose | 18:36 |
| yashgaroth | XK column? | 18:36 |
| delinquentme | yeah. http://www.ebay.com/itm/Pharmacia-Biotech-XK-16-20-chromatography-Column-Excellent-GE-Amersham-/321410626909?pt=LH_DefaultDomain_0&hash=item4ad590f55d | 18:36 |
| delinquentme | yashgaroth, !!!!!! | 18:36 |
| delinquentme | damnit hahah | 18:36 |
| delinquentme | I'd gladly pay you for some if its under market value :D | 18:37 |
| yashgaroth | it won't be, buy it off ebay, that's a good price | 18:37 |
| delinquentme | ah alright. thanks anyhoo | 18:37 |
| yashgaroth | you think I can buy them from GE for less than that? because laffo | 18:37 |
| kanzure | dingo: were you GE or GM? | 18:38 |
| yashgaroth | delinquentme I'm not sure how fully you appreciate that biotech stuff is absurdly expensive | 18:39 |
| delinquentme | yashgaroth, I'm getting hints of it. The prices of the fibronectin I was gonna purify are obscene. | 18:40 |
| yashgaroth | I thought you was purifying your own fibronectin out of corpses | 18:40 |
| delinquentme | piggie blood | 18:41 |
| yashgaroth | or whatever | 18:41 |
| delinquentme | I was also looking for human femurs for other reasons though | 18:41 |
| yashgaroth | yeah they're good to have around | 18:41 |
| delinquentme | yeah. Could make for a decent bioreactor | 18:41 |
| yashgaroth | well anyway you're gonna need more than a single heparin purification, lotta shit in blood binds heparin | 18:42 |
| delinquentme | I was thinking decellularizing the vasculature and then using that piping system to distribute haematopoetic stem cells | 18:42 |
| yashgaroth | uh huh | 18:42 |
| delinquentme | yeah I've got the protocol ... just no paying clients | 18:42 |
| yashgaroth | you want someone to pay you to dissolve their blood vessels? | 18:43 |
| delinquentme | sorry nah, two separate projects. One was " people who would buy fibronectin " | 18:43 |
| delinquentme | the other is " how to get osteoblasts / HSCs to maintain + product blood " | 18:44 |
| yashgaroth | try high-pressure sales techniques, like stab them and then say 'would you like to buy my miracle wound healing powder?' | 18:45 |
| yashgaroth | if they say no you can still take their money! | 18:45 |
| yashgaroth | anyway kanzure there's also tangential flow filtration, which is awesome, but again adapting it to micro scale would be a challenge | 18:48 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=4d334d80 Bryan Bishop: brief mention of tangential flow filtration >> http://diyhpl.us/diyhpluswiki/diybio/microfluidics/ | 18:48 |
| yashgaroth | assuming you want cells producing tiny amounts of antibody, you can keep them in a chamber, and then flow that with some back-pressure and push antibodies through the membrane while keeping the cells in one place | 18:48 |
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| kanzure | oh, keeping the cells on-chip makes sense, i was also thinking of just loading up whatever liquid from some other process | 18:49 |
| kanzure | on-chip cell culture makes more sense though | 18:49 |
| yashgaroth | I assumed that's what you were going for, since you'd be making tiny amounts of antibody | 18:49 |
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| yashgaroth | either way, tangential flow/ultrafiltration is the biggest thing to happen in purification since...well, a while | 18:50 |
| kanzure | no idea if it would be tiny or not- add in some parallelism and suddenly you have large cultures producing antibodies | 18:50 |
| yashgaroth | but then why microfluidicize it | 18:50 |
| kanzure | the parts that need to be microsized are the parts that cost an annoying amount | 18:51 |
| kanzure | for doing normal biology lab things | 18:51 |
| kanzure | instead of paying $500 per pcr machine you could just print them out | 18:52 |
| yashgaroth | PCR is an exception because you're regularly working with picograms | 18:52 |
| kanzure | sonoporation can also work on a chip | 18:52 |
| kanzure | separation stuff can work | 18:52 |
| yashgaroth | well I'd focus mainly on DNA then | 18:53 |
| yashgaroth | tangential flow is nice for that, you can separate decently-sized strands away from dNTPs, buffer salts etc | 18:54 |
| seba- | why would a PCR machine cost $500 | 18:54 |
| seba- | lol | 18:54 |
| dingo | kanzure: GM | 18:54 |
| kanzure | seba-: yeah it's stupid isn't it? they actually go for $20k | 18:54 |
| kanzure | dingo: damn | 18:54 |
| seba- | kanzure, a PCR machine should be around $150 | 18:54 |
| seba- | if you make it at home | 18:55 |
| kanzure | you can make one for <$10 | 18:55 |
| seba- | yeah | 18:55 |
| seba- | with various baths | 18:55 |
| seba- | lol | 18:55 |
| kanzure | not even | 18:55 |
| kanzure | the lightbulb method doesn't require multiple baths | 18:55 |
| seba- | ok | 18:55 |
| seba- | i meant $150 for a proper aluminium block/peltier | 18:55 |
| kanzure | proper | 18:55 |
| kanzure | there's all sorts of other equipment that is expensive in a lab that you could build on a flat surface instead | 18:56 |
| seba- | like | 18:56 |
| kanzure | http://diyhpl.us/wiki/diybio/microfluidics/ | 18:56 |
| kanzure | http://diyhpl.us/~bryan/papers2/microfluidics/ | 18:57 |
| kanzure | oh i forgot cell sorting | 18:58 |
| kanzure | that falls under separation though | 18:58 |
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| kanzure | hrm, so the really interesting stuff only happens when you can do dna sequencing and synthesis | 19:01 |
| kanzure | "Utau is known mostly as being a free clone of the much more popular and mature Vocaloid software" | 19:08 |
| kanzure | for comparison, | 19:09 |
| kanzure | vocaloid: http://www.youtube.com/watch?v=_JGaQ3g8WU4 | 19:09 |
| kanzure | utau: http://www.youtube.com/watch?v=nCqy27QrqZA | 19:09 |
| gradstudentbot | I don't have enough data to form a hypothesis. | 19:12 |
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| kanzure | i gave you *two* samples, isn't that enough | 19:20 |
| seba- | http://phys.org/news95869196.html | 19:29 |
| kanzure | .title | 19:29 |
| yoleaux | Researchers Use Smallest Pipette to Reveal Freezing 'Dance' of Nanoscale Drops | 19:29 |
| seba- | look how big it is | 19:29 |
| kanzure | making tiny tips is hard | 19:30 |
| kanzure | just ask the afm users | 19:30 |
| kanzure | well, annoying, not really hard | 19:30 |
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| nmz787 | ok hi | 20:13 |
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| gene_hacker | by doing interesting stuff with DNA synthesis and sequencing do you mean making an ultra-parallel computer for cracking crypto/mining bit coin? | 20:48 |
| kanzure | gene_hacker: microelectronics would be better at mining bitcoin, http://diyhpl.us/wiki/homecmos/bitcoin/ | 20:49 |
| kanzure | dna synthesis is too slow for bitcoin mining | 20:50 |
| gene_hacker | probably, but you can still use them to crack crypto | 20:51 |
| kanzure | various SAT problems i guess, yeah | 20:51 |
| gene_hacker | DNA computers are supposed to have some nice scaling laws two | 20:51 |
| kanzure | reason i mentioned dna synthesis "to do anything interesting" is biology reasons | 20:53 |
| kanzure | once you can do dna synthesis you can inject dna into cells and get whatever wacky proteins, antibodies, or whatever you please | 20:53 |
| gene_hacker | but if you convince the bitcoin people that DNA synthesis and sequence is worth it... | 20:55 |
| kanzure | i think we could convince them that asic/microelectronics fabrication is worth it | 20:56 |
| kanzure | there's some math i need to figure out to prove that it's cost effective | 20:56 |
| kanzure | compared to doing an asic batch run at MOSIS or some other wafer fab | 20:56 |
| kanzure | microelectronics fabrication is practically the same method as microfluidics, if you are using contact lithography (which is fine for 1-100 micron features) | 20:57 |
| kanzure | i mean, if you build a mask via photolithography, which you then use to stamp a wafer or w/e | 20:57 |
| kanzure | (or you can possibly laser cut a wafer directly if you cared a lot..) | 20:57 |
| gene_hacker | microelectronics fabrication is quite different than microfluidics fabrication | 20:58 |
| gene_hacker | microfluidics tend to be a lot bigger than most things on a microchip | 20:58 |
| kanzure | you don't need nanometer features for microelectronics | 20:58 |
| kanzure | first few microchips were using 200 micron transistors | 20:58 |
| kanzure | (1960s) | 20:59 |
| kanzure | photomask chemistry might be different, but once you have something the right size (existing mask?) you have more options | 21:02 |
| nmz787 | gene_hacker: well there /are/ jumping genes, so i presume eventually we'll be able to edit DNA with DNA programmed stuff | 21:02 |
| kanzure | "eventually" is "not in the next 5 years" | 21:02 |
| gene_hacker | you don't need nanometer feature resolution, but it helps | 21:03 |
| nmz787 | gene_hacker: you need the DNA synthesis first though to optimize all the biological 'logic gate' precedent papers that are around | 21:03 |
| nmz787 | such that they work when linked into massive systems | 21:03 |
| kanzure | if you have dna synthesis then you can just build proteins/antibodies which are going to be useful and valuable anyway | 21:03 |
| nmz787 | of which could be self-editing programs/logic-functions | 21:03 |
| gene_hacker | well logic gates are one way to do it, but there are better ways of solving problems with DNA | 21:03 |
| nmz787 | well whatever, there's some operation you want to do that's probably recursive or something | 21:04 |
| nmz787 | so you need to verify the base function first, and that process is really slow right now | 21:05 |
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| kanzure | you killed him | 21:06 |
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| kanzure | fenn: summon | 21:08 |
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| fenn | moooooo... | 21:32 |
| kanzure | fenn: reasons not to use belts? | 21:34 |
| kanzure | or am i full of shit | 21:34 |
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| fenn | not for micron resolution; the belts arent precise enough | 21:35 |
| fenn | maybe if you had a linear optical encoder (glass rule) | 21:35 |
| kanzure | nmz787 is trying to convince me about cannibalizing an existing commodity microscope | 21:36 |
| kanzure | instead of building our own stuff, stages, etc. | 21:36 |
| fenn | that sounds easier than building everything | 21:36 |
| kanzure | e.g., place gear on microscope knob, belt, stepper to control | 21:36 |
| kanzure | well, i don't want this to be dumpster diving and repurposing | 21:36 |
| fenn | are there no standard microscope designs? | 21:37 |
| nmz787 | fenn: how about a gear to gear from the coaxial stage knob on most any microscope to a geared stepper motor that is microstepping (just cause the microcontroller can) (28byj-48 stepper) | 21:37 |
| kanzure | there's "openlabtools" that you were complaining about, http://openlabtools.eng.cam.ac.uk/Instruments/Microscope/images/microscope.png | 21:37 |
| kanzure | or maybe that was me that was complaining | 21:37 |
| fenn | nmz787: i don't like gears for motion control.. introduces backlash for no good reason, and they're noisy | 21:37 |
| kanzure | nah we can have it play hatsune miku songs when it's stepping | 21:38 |
| nmz787 | yeah, but what's a better way? | 21:38 |
| nmz787 | i was thinking a one-time calibration | 21:38 |
| fenn | well since this is optical you might be fine with gears and a spring | 21:38 |
| nmz787 | go to bottom-left (home) then microstep all the way to the right, then go home, then microstepp all the way to the top.... slowly enough to get images of each microstep | 21:38 |
| nmz787 | and also maybe the backlash at each location | 21:39 |
| kanzure | one of the hypothetical advantages of not using an existing microscope that i was contemplating is that you get to make whatever frame you need | 21:39 |
| kanzure | with as much clearance as you want | 21:39 |
| fenn | images of what? | 21:39 |
| kanzure | (none of that weird curvy neck shit. i don't trust those scopes.) | 21:39 |
| nmz787 | then either try using that to calibrate, or use it to get good averages for correction factors | 21:39 |
| nmz787 | images of a laser printed grid reticle | 21:40 |
| nmz787 | laser printers can do something like 20 or 50 micron lines | 21:40 |
| kanzure | so, how much would it cost to buy both the gears/belts and the threaded rod/washers/screws | 21:40 |
| nmz787 | seems more accesible than a shelf-bought grid | 21:40 |
| fenn | uh, don't use a laser printer as your reference measurement | 21:40 |
| kanzure | there's cheap slides that provide micrometer calibration for microscopes | 21:41 |
| nmz787 | i didn't find any that were the right size and design for cheap | 21:41 |
| kanzure | http://www.amazon.com/AmScope-MR400-Micrometer-Calibration-Microscopes/dp/B005KVGAAS | 21:42 |
| fenn | you could use a reject silicon wafer :P | 21:42 |
| nmz787 | its really annoying that I can't even tell if the ebay scopes have infinity objectives on them | 21:42 |
| kanzure | it's based on tube length | 21:42 |
| nmz787 | silicon doesn't have a grid on it though | 21:42 |
| kanzure | the 270mm tubes or something are the infinity corrected ones. and presumably the objectives say whether or not they are for that tube size. | 21:42 |
| nmz787 | i measured a lot of laser printed lines a while ago when i made a test lithography mask on transparency paper | 21:43 |
| nmz787 | film | 21:43 |
| kanzure | erm, *those tubes are the ones that fit infinity corrected objectives | 21:43 |
| nmz787 | it was pretty decent | 21:43 |
| fenn | a reject wafer would have a grid of chips on it | 21:43 |
| kanzure | or you can get the $30 slide i just linked to | 21:43 |
| nmz787 | yeah but you don't know the dimensions | 21:43 |
| fenn | the slide doesn't cover the whole range of motion | 21:43 |
| fenn | (or does it?) | 21:43 |
| kanzure | "1mm Total Length Subdivided into 100 Divisions, Each Division is 0.01mm Across" | 21:44 |
| kanzure | "Just in case you can't fucking divide" | 21:44 |
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| fenn | let me get out my atm machine card | 21:44 |
| nmz787 | No I guess not | 21:45 |
| kanzure | http://www.pyser-sgi.com/graticules/stage-micrometers-calibration-scales-grids/stage-micrometers-grids-s-series/s28-stage-counting-grid-0-01mm-squares-detail | 21:45 |
| gradstudentbot | If I write this paper, then maybe I can use that as my thesis? | 21:45 |
| kanzure | "0.01mm grid / 0.2 x 0.2mm overall" | 21:45 |
| kanzure | hrm | 21:46 |
| nmz787 | with 1 to 10 micron features that is still a lot of space | 21:46 |
| kanzure | huh, what about this one? | 21:46 |
| kanzure | http://www.pyser-sgi.com/graticules/stage-micrometers-calibration-scales-grids/stage-micrometers-grids-s-series/s7-england-finder-slide-detail | 21:46 |
| gradstudentbot | I'll need to pull an all-nighter. | 21:46 |
| nmz787 | problem might be with breaking out the lines to microtubes | 21:46 |
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| nmz787 | but then again, you could go into open-loop in those regions | 21:47 |
| fenn | is this some magic eye thing | 21:47 |
| kanzure | no i think they just wrote a bunch of numbers in each cell because ?? | 21:47 |
| kanzure | it's curious that most micrometer slides are only for a small mm^2 region | 21:47 |
| fenn | numbers would make a lot more sense | 21:48 |
| fenn | they probably just expose photographic emulsion directly on the slide through a microscope | 21:48 |
| kanzure | "if you can't see all the detail at once, there's no point" | 21:48 |
| kanzure | yeah, but you could just move the slide and expose again | 21:48 |
| fenn | but then you have to ensure that each sub-grid is precisely aligned | 21:48 |
| fenn | before you know it you are back at the micron laser plotter | 21:49 |
| kanzure | i shouldn't pussy out by buying both sets of actuators (gears/belts and screws) | 21:49 |
| nmz787 | that's called a stepper | 21:49 |
| nmz787 | a wafer stepper | 21:49 |
| kanzure | yes i know what a stepper is | 21:49 |
| kanzure | wtf | 21:49 |
| fenn | silicon chips don't have to be precisely aligned to each other | 21:49 |
| fenn | making precise things is easy; making accurate things is easy; making precise and accurate things is hard | 21:50 |
| nmz787 | they still use interferometers on the axes | 21:50 |
| nmz787 | kanzure: want to start off the night by buying both of those? | 21:50 |
| nmz787 | the latter seems like it would be computationally more work | 21:51 |
| fenn | gears belts and screws is three things | 21:51 |
| nmz787 | to track | 21:51 |
| kanzure | no prices on the page | 21:51 |
| nmz787 | yeah | 21:51 |
| kanzure | so no | 21:51 |
| kanzure | i think we should separate the project into two parts: | 21:51 |
| kanzure | (1) the machine we want to build | 21:52 |
| kanzure | (2) laser diode, lcd projector, dmd projector lithography things through whatever microscopes you already have | 21:52 |
| nmz787 | I think that openlabstools had a FOV calculator | 21:52 |
| nmz787 | there's also all the software though too | 21:53 |
| nmz787 | soft/firm | 21:53 |
| kanzure | #2 would probably mean "buy some photoresist" and maybe a way to mount something | 21:53 |
| nmz787 | #2 still needs a reticle | 21:53 |
| kanzure | the full-slide grid? or partial-slide grid | 21:54 |
| kanzure | that amazon one looked ok for basic calibration | 21:54 |
| nmz787 | the amazon one would prove the concept i think, and maybe draw others into that part of the project | 21:55 |
| kanzure | what others | 21:55 |
| kanzure | fenn: what material did you think the frame should be made out of? | 21:56 |
| gradstudentbot | Can I take a nap yet? | 21:56 |
| nmz787 | "Casio EX-ZR100" | 21:56 |
| nmz787 | up to 1000FPS | 21:56 |
| nmz787 | but most likely not over USB | 21:56 |
| fenn | the same material as everything else, but preferably cast iron | 21:56 |
| fenn | that's the benefit of using a premade microscope | 21:57 |
| fenn | vibration may not matter in practice though, i have no idea | 21:58 |
| kanzure | nmz787: er, why? amazon does not list this as a linux-compatible camera, so they probably don't think it's important, and they probably didn't check streaming capability | 21:58 |
| kanzure | and it has an lcd hah | 21:58 |
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| nmz787 | oh cool | 21:59 |
| nmz787 | http://www.raspberrypi.org/new-camera-mode-released/ | 21:59 |
| nmz787 | 90 FPS | 21:59 |
| fenn | the casio is not a webcam and definitely doesn't stream at 1000fps | 21:59 |
| fenn | it is a neat toy tho | 21:59 |
| kanzure | the openlabtools microscope's frame just seems much easier to work with than a curvy-neck microscope, | 21:59 |
| kanzure | http://openlabtools.eng.cam.ac.uk/Instruments/Microscope/images/microscope.png | 21:59 |
| kanzure | look at all that free space to put crap | 21:59 |
| gradstudentbot | Anyone else think pol II looks like a butt? | 22:00 |
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| fenn | those rod ways are a joke | 22:01 |
| fenn | why build a t-slot frame and then suspend two toothpicks from pieces of plastic | 22:01 |
| kanzure | they had "10 people working on this for 10 weeks" | 22:02 |
| fenn | seriously what is it with people and t-slot cubes | 22:02 |
| kanzure | so i am gonna go ahead and assume they are brain damaged | 22:02 |
| fenn | i hope it works better than a bent paperclip and a drop of water | 22:02 |
| kanzure | t-slot structure has got to be better than attaching to http://www.coslabindia.com/HL-55.jpg | 22:03 |
| fenn | does it have X or Y axis drive? or only motorized Z? | 22:04 |
| nmz787 | all axes | 22:04 |
| gradstudentbot | I lost my pipette. | 22:04 |
| nmz787 | all 3 | 22:04 |
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| nmz787 | fenn: so what material then? | 22:06 |
| fenn | if you want to throw huge gobs of cash you could use epoxy granite concrete and linear ways | 22:07 |
| fenn | i'm not sure why they use "crossed roller" ways in optical stuff | 22:07 |
| nmz787 | i think the idea is to keep costs practical, i think unde $1k | 22:08 |
| kanzure | over $1k is okay | 22:08 |
| fenn | is that just a way of saying "dovetail slides, but with rollers"? | 22:08 |
| nmz787 | fenn: that is your question to answer | 22:08 |
| nmz787 | my CAD PIPE is redirected to fenn | 22:09 |
| fenn | my optics experience consists of burning ants with a magnifying glass | 22:09 |
| kanzure | perfect | 22:09 |
| nmz787 | i've been trying to learn for a while | 22:09 |
| kanzure | nmz787: do these guys have any good pics of their microscopy in action? | 22:09 |
| fenn | so i was thinking a solar sand sinterer would be cool | 22:09 |
| nmz787 | i have all the optical parts for the openlabtools scope i believe | 22:09 |
| nmz787 | there was 1 or 2 pics | 22:09 |
| fenn | one with better optics than that projection screen tv fresnel lens | 22:09 |
| kanzure | because the bug on this page sucks http://openlabtools.eng.cam.ac.uk/Instruments/Microscope/Optics/ | 22:09 |
| kanzure | this is just a fucking awful pic to advertize your microscope | 22:09 |
| nmz787 | showing chromatic aberration i believe | 22:09 |
| nmz787 | either from lack of oil, or from using the wrong tube lens | 22:10 |
| nmz787 | i think/hope it was chromatic | 22:10 |
| fenn | a dobsonian telescope would probably work for fine sintering | 22:10 |
| kanzure | and i hate how nobody does calibration or takes measurements | 22:10 |
| nmz787 | as using laser is monochromatic so wont mess up like that | 22:10 |
| kanzure | well that's fine, but that bug is way bigger than 1 micron | 22:10 |
| kanzure | or 10 microns | 22:10 |
| kanzure | or 100... | 22:11 |
| fenn | is there supposed to be a video or something? | 22:11 |
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| nmz787 | i dont think so | 22:11 |
| kanzure | http://openlabtools.eng.cam.ac.uk/Instruments/Microscope/media/OLT_Microscope.mp4 | 22:12 |
| fenn | nevermind, i dunno why it didnt render at all in dillo | 22:12 |
| nmz787 | https://groups.yahoo.com/neo/groups/Microscope/conversations/topics/33567 | 22:13 |
| kanzure | .title | 22:13 |
| yoleaux | Yahoo Groups | 22:13 |
| kanzure | fuck you yahoo groups | 22:13 |
| fenn | can't they fix chromatic aberration by using an RGB LED and taking separate pictures? | 22:14 |
| fenn | or is that too high tech | 22:14 |
| gradstudentbot | Yeah, but his PI wrote his dissertation. | 22:14 |
| fenn | am i a genius or is everyone just a moron | 22:15 |
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| kanzure | neither, you are simply stuck in the seventh circle of super hell | 22:15 |
| kanzure | copy of their video (their server was downloading too slow for me..) http://diyhpl.us/~bryan/irc/openlabtools-microscope/OLT_Microscope.mp4 | 22:16 |
| nmz787 | it wouldn't work well for living subjects | 22:16 |
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| fenn | oh well, you would either get motion blur from 1/30 framerate or 1/90 framerate | 22:16 |
| fenn | assuming your stepper can refocus fast enough | 22:16 |
| kanzure | were you holding off on the stepper mount plates because we didn't know which stepper? | 22:17 |
| nmz787 | unless you synched and stopped just before the exposure | 22:17 |
| kanzure | this video is way too big for what it is showing | 22:18 |
| fenn | http://www.designworldonline.com/When-to-Choose-Crossed-Roller-Bearings/ | 22:18 |
| fenn | ugh it's not streamable? | 22:19 |
| fenn | "Cage creep can be prevented by studs that roll into the raceways depressions. | 22:20 |
| nmz787 | fenn, actually their video says 8-bit RGB LED | 22:20 |
| nmz787 | so they simply failed to get HDR images | 22:20 |
| fenn | <insert sarcastic WWF methamphetamine reference here> | 22:20 |
| nmz787 | or HD-focus | 22:20 |
| fenn | Z-stacking is pretty common in macro photography; i figured it was also standard practice in computer-controlled microscopy | 22:21 |
| nmz787 | fenn: is 3d-printed bad for material? | 22:21 |
| fenn | yes | 22:21 |
| fenn | but the rod ways are particularly bad | 22:21 |
| nmz787 | fenn: i think you understimate CNC-scopy | 22:21 |
| nmz787 | wait | 22:21 |
| nmz787 | overestimate | 22:21 |
| fenn | superestimate | 22:21 |
| kanzure | actually-estimate | 22:21 |
| nmz787 | ultraestimate | 22:21 |
| kanzure | i don't think these guys were getting microscopic resolution | 22:22 |
| fenn | yeah they should have taken photos of a CD or something | 22:22 |
| kanzure | and besides, if they were really serious, they would submerge the whole machine in oil to prove their determination | 22:22 |
| fenn | not "this hairy bug i pulled out of my butt-crack" | 22:22 |
| nmz787 | that 80/20 t-slot seems pricey | 22:23 |
| fenn | that is openmakerbeamslot | 22:23 |
| kanzure | *beamslut | 22:23 |
| fenn | sirbeamsalot | 22:23 |
| kanzure | ah without the slut shaming. nice. | 22:23 |
| nmz787 | decaocular microscope with interleave raspberry pi cameras each at 90FPS | 22:24 |
| nmz787 | ULTRA | 22:24 |
| nmz787 | DECA | 22:24 |
| nmz787 | LAURYL | 22:24 |
| kanzure | are you okay? | 22:24 |
| fenn | sulfonuramidoscope? | 22:24 |
| nmz787 | oh, wait DOCECYL | 22:24 |
| nmz787 | DODECYL | 22:24 |
| nmz787 | ** | 22:24 |
| nmz787 | fenn: please make some recommendations before the night is through, or at least some things that might be the right direction if you aren't interested enough to spend more time on this | 22:25 |
| nmz787 | we need you fenn! | 22:26 |
| nmz787 | (or at least I think we do) | 22:26 |
| fenn | buy a microscope with a vertical camera port | 22:26 |
| fenn | add a beam splitter for whatever extra crap you want to add | 22:26 |
| fenn | i know you lose power but i doubt laser power is the limiting factor | 22:27 |
| nmz787 | for the custom job, would 3D printing be useful for design/prototyping stage? | 22:27 |
| nmz787 | what about for lense holders? | 22:28 |
| nmz787 | even for them just prototyping | 22:28 |
| fenn | you can just buy this stuff | 22:28 |
| nmz787 | are CNC mills as easy to get parts out of as a 3D printer? | 22:28 |
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| nmz787 | is the design strategy different, or just the CAM file? | 22:28 |
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| kanzure | you give the machine shop your cad file, never a cam file | 22:28 |
| nmz787 | CAM compiler | 22:28 |
| fenn | no, and yes, and no | 22:29 |
| fenn | cnc is a lot harder to think about than 3d printing | 22:29 |
| fenn | that's kinda the point | 22:29 |
| fenn | if it were easy we wouldn't need 3d printers | 22:29 |
| gradstudentbot | I don't remember the paper, but someone definitely did that. | 22:29 |
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| fenn | huh that crossed roller way is pretty neat | 22:31 |
| fenn | it's just a 90 degree v-groove | 22:32 |
| fenn | someone should do a t-slot thing like that | 22:32 |
| kanzure | it would be nice to do the machine shop run al lat once | 22:33 |
| kanzure | *all at once | 22:33 |
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| fenn | i'm not sure what you are planning on machining; all this is pretty standard microscope stuff, no? | 22:34 |
| kanzure | i am very confused about priorities | 22:34 |
| fenn | you need: a camera mount, a laser mount, a motorized stage | 22:34 |
| kanzure | the xy stage needs to be mounted to something | 22:34 |
| kanzure | and the z has to be mounted somewhere | 22:34 |
| nmz787 | and a microscope in between | 22:34 |
| fenn | the laser has independent focus mechanism, so why do you need a Z | 22:35 |
| kanzure | microscope tube and objective can be mounted on the z | 22:35 |
| nmz787 | with adjustments everywhere for focus and if its our build I'd think tilt | 22:35 |
| nmz787 | or that would all need to be precisely machined stuff so the angles were right | 22:35 |
| kanzure | oops, stage would have z | 22:35 |
| kanzure | you want z for the normal reasons you have z on a microscope | 22:35 |
| kanzure | i don't see why it would be different just because you have a laser in use for less than 100% of the time? | 22:36 |
| nmz787 | well there are two laser routes, one is beam splitter in the microscope (laser down the ocular of a bino scope) | 22:36 |
| nmz787 | and a bluray module mounted next to the objective | 22:36 |
| nmz787 | two different tests | 22:36 |
| kanzure | huh? | 22:36 |
| nmz787 | adjustable focus laser mated to a binocular scope's right-eye ocular... camera on the other ocular | 22:37 |
| kanzure | blah oculars.. | 22:37 |
| kanzure | is that really necessary | 22:38 |
| nmz787 | well we could call that area something else | 22:38 |
| nmz787 | the tube lens i suppose | 22:38 |
| nmz787 | lenses | 22:38 |
| kanzure | like why do we have to have pieces that are fitted for human eyes- who cares | 22:38 |
| nmz787 | that was just my labelling from the cannibalizing idea | 22:38 |
| nmz787 | don't you care about robot eyes (cameras and lasers) | 22:39 |
| kanzure | these just seem annoying: http://www.microscope.com/media/catalog/product/cache/2/image/9df78eab33525d08d6e5fb8d27136e95/m/e/meiji_mt6000_fluorescence_microscope_eyepieces.png | 22:39 |
| fenn | you can pull them out of the tube they sit in | 22:40 |
| fenn | then it's just like a camera port | 22:40 |
| kanzure | ah | 22:40 |
| fenn | the ocular lenses usually help in mounting a webcam though because webcams have similar focal length and focusing range as human eyes | 22:40 |
| fenn | or so i hear | 22:41 |
| fenn | you also should be able to pop off the rubber thingies | 22:41 |
| kanzure | good | 22:41 |
| nmz787 | yeah, maybe a set screw | 22:41 |
| kanzure | why are there only two? | 22:41 |
| kanzure | why not 8 | 22:41 |
| fenn | because we're humans, not spiders | 22:41 |
| * nmz787 nods | 22:42 | |
| kanzure | ugh | 22:42 |
| nmz787 | shew spider! | 22:42 |
| fenn | if you want to shoot lasers or use a camera, you're expected to use a microscope with a camera port | 22:42 |
| kanzure | yeah but i think we need more than just a trinocular microscope | 22:42 |
| fenn | but those tend to cost a lot more for reasons that are beyond my comprehension | 22:42 |
| kanzure | "because nobody knows how to insert a prism" | 22:43 |
| fenn | they tend to be much bigger and have more stuff | 22:43 |
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| kanzure | "elbow" http://www.truetex.com/zeiss_opmi_elbow_3.jpg | 22:44 |
| kanzure | http://www.truetex.com/zeiss_opmi_elbow_2.jpg | 22:44 |
| fenn | that is not what i mean | 22:44 |
| kanzure | i know | 22:45 |
| fenn | i'm talking about https://en.wikipedia.org/wiki/File:Microscope_And_Digital_Camera.JPG | 22:45 |
| kanzure | .title http://www.truetex.com/micad.htm | 22:45 |
| yoleaux | Making Digital Camera Microscope Adapters | 22:45 |
| nmz787 | tri would only be needed for .... | 22:46 |
| nmz787 | idk, if the computer was broken? | 22:46 |
| nmz787 | we wanted another color laser | 22:46 |
| fenn | a penny would have been a good test of the british microscope | 22:46 |
| nmz787 | a spectrometer port | 22:46 |
| fenn | oh but it's transmission, nevermind | 22:46 |
| gradstudentbot | I was searching for a new particle that alters gene expression, didn't find it, but didn't refute it's existence either. But then some other asshole professor at another school found it. | 22:47 |
| fenn | most of that truetex stuff is for mounting the camera to anything else | 22:47 |
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| fenn | honestly a lot of it can be done with a piece of pvc pipe | 22:49 |
| kanzure | that page has a bunch of content | 22:49 |
| fenn | but "optics!" and "high quality!" | 22:49 |
| kanzure | pvc pipe sounds good to me | 22:49 |
| fenn | yeah i've read it before | 22:49 |
| kanzure | lolwtf "Adapters incorporating optical elements are more complex and typically cost $500 to $950, including the optical elements. Complete kits for medical and scientific instruments, with custom mechanical, optical, and electronic components, range from $800 to $6000." | 22:50 |
| fenn | are you going to believe the guy who makes his living selling adapters | 22:51 |
| kanzure | i am sure that's what he sells them for... | 22:51 |
| kanzure | what a booming market | 22:51 |
| kanzure | literally dozens of microscopes aorund the globe | 22:52 |
| fenn | you fail at sarcasm | 22:52 |
| kanzure | hm? of course i'm not going to believe him | 22:52 |
| kanzure | but also his market sucks | 22:52 |
| fenn | not everyone can make the next snapchat | 22:52 |
| kanzure | that doesn't mean you should support the microscope monopolists | 22:53 |
| kanzure | isn't it just zeiss, olympus, nikon that are making "the good ones"? | 22:53 |
| kanzure | everything else does not seem to be micro | 22:53 |
| fenn | I modify the the Microsoft Lifecam Cinema (720p HD) and Microsoft Lifecam Studio (1080p HD) cameras for scientific and medical instrumentation. The Lifecams are USB cameras with amazing high-definition video performance, especially considering their street price of about $50 to $100. They also have the rare virtue among webcams of being housed in a cylindrical metal shell, so they can be easily | 22:54 |
| fenn | fitted into the cylindrical geometry typical of optical instrumentation, in many cases with no modifications, using a relatively simple mechanical adapter. | 22:54 |
| nmz787 | I think someone asked for this a while ago, maybe gene_hacker http://diyhpl.us/~nmz787/pdf/Efficient_Assembly_of_Threaded_Molecular_Machines_for_Sequence-Specific_Synthesis.pdf | 22:54 |
| gene_hacker | oh no, I was posting that | 22:54 |
| kanzure | fenn, wouldn't it be better to just skip all the weirdo tubes, adapters, etc. completely, and just use your own pvc pipe stuff.. | 22:55 |
| fenn | i'd rather start with a cylindrical camera at least | 22:55 |
| fenn | "Just tested the Microsoft Lifecam Studio; it works out of the box on | 22:58 |
| fenn | Ubuntu 10.10 (both video and microphone worked perfectly). I tested | 22:58 |
| fenn | using cheese, camorama and skype." | 22:58 |
| nmz787 | I haven't had time to sit and read this one http://diyhpl.us/~bryan/papers2/paperbot/Reproductive%20ectogenesis%3A%20The%20third%20era%20of%20human%20reproduction%20and%20some%20moral%20consequences.pdf | 22:58 |
| fenn | "One thing I did notice is that when I run v4l2ucp, the "Exposure,Auto" | 22:59 |
| fenn | setting has four modes (Auto, Manual, Shutter Priority and Aperture | 22:59 |
| fenn | Priority) but only Manual and Aperture Priority work (the other two | 22:59 |
| fenn | result in a dialog saying "Unable to set Exposure,Auto; input/output | 22:59 |
| fenn | error"." | 22:59 |
| kanzure | http://www.amazon.com/Microsoft-LifeCam-Studio-1080p-Webcam/dp/B0042X8NT6 | 22:59 |
| fenn | manual exposure is what you want anyway | 22:59 |
| nmz787 | raspberry pi cam should work | 22:59 |
| nmz787 | i feel like i saw someone using the GPU for opencv stuff too | 22:59 |
| kanzure | CAM? | 22:59 |
| kanzure | the point was that this camera is already fitted to the right ports | 23:00 |
| nmz787 | maybe I am wrong about using GPU accell, maybe it was just for grabbing the video/images | 23:00 |
| nmz787 | that binary blob | 23:00 |
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| kanzure | hm, maybe the concept of having multiple people working on design is stupid | 23:00 |
| kanzure | it is clear that there is no ability to get coherent | 23:00 |
| kanzure | and then you end up with stupid shit | 23:01 |
| fenn | burbledeeburbledeebahbahblooo | 23:01 |
| kanzure | like openlabtools' stuff | 23:01 |
| fenn | haven't you heard of "design by committee" | 23:01 |
| kanzure | it's not a committee if... well. uh. | 23:01 |
| nmz787 | i think there aren't enough ppl on this 'team' | 23:01 |
| kanzure | is it? | 23:01 |
| fenn | it's the latest executive mangement craze, patterned after the "waterfall pattern" pattern | 23:01 |
| kanzure | hahaha yeah add more people, that'll help | 23:01 |
| kanzure | (it wont) | 23:01 |
| nmz787 | i am serious | 23:02 |
| nmz787 | there isn't enough discussion | 23:02 |
| nmz787 | not enought input | 23:02 |
| nmz787 | not enough direction | 23:02 |
| nmz787 | (you cried for it earlier) | 23:02 |
| kanzure | i have no idea what i could say to convince you otherwise | 23:02 |
| nmz787 | get some more ppl who know CAD, know CNC, know optics | 23:02 |
| kanzure | all three of us know cad | 23:03 |
| kanzure | i don't think anyone knows optics | 23:03 |
| nmz787 | what CAD tool should be used? | 23:03 |
| kanzure | brlcad | 23:03 |
| kanzure | python-brlcad if possible, but not necessary | 23:03 |
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| kanzure | openscad is not end of world | 23:03 |
| kanzure | but sorta is | 23:03 |
| fenn | brl-cad does ray tracing but does it know about chromatic aberration? | 23:03 |
| kanzure | i asked brlcad about that and he said - uh | 23:04 |
| kanzure | well | 23:04 |
| fenn | "try it and find out!" | 23:04 |
| kanzure | 10:10 < brlcad> kanzure: it won't do some optical effects like spectrum diffraction (prism effects) | 23:04 |
| fenn | ok | 23:04 |
| kanzure | 10:13 < brlcad> ray tracing theory doesn't generally including wave effects like diffraction and interference | 23:05 |
| kanzure | 10:13 < brlcad> our multispectral library might have that capability, but I honestly haven't looked at it in many years | 23:05 |
| kanzure | 10:13 < brlcad> our multispectral library does track packets of spectrum as they propagate, but I don't know to what extent | 23:05 |
| fenn | so you can actually ray trace a hyperspectral image? | 23:05 |
| kanzure | 10:16 < brlcad> fwiw, I don't believe povray does diffraction either | 23:05 |
| kanzure | 10:22 < brlcad> mildly relevant: http://brlcad.org/gallery/renderings/lightbulb/lightbulb | 23:06 |
| kanzure | 10:23 < brlcad> had a rendering of a gci-modeled fresnel lens that was modeled in brl-cad, but I can't find the optical rendering | 23:06 |
| kanzure | 10:23 < brlcad> kanzure: we also have http://brlcad.org/xref/source/src/proc-db/lens.c which might be interesting | 23:06 |
| kanzure | 10:24 < brlcad> (it's one of brl-cad's dev tools, creates lens geometry) | 23:06 |
| fenn | well i remember seeing the magnified LED in the ronja animation | 23:06 |
| fenn | so the newtonian optics seems to work well enough | 23:07 |
| nmz787 | wouldn't the chromatic effect just be a LUT of color vs refractive index? | 23:07 |
| kanzure | jblake recommends pbrt (physics-based ray tracer) | 23:07 |
| fenn | that light bulb has some weird triangular artifacts | 23:08 |
| kanzure | well, at minimum, lens.c looks interesting | 23:10 |
| kanzure | even if not using their ray tracer | 23:10 |
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| fenn | huh so OLT microscope is top-lit (not transmission) | 23:13 |
| fenn | also they have no condenser lens | 23:13 |
| fenn | i wonder if anyone who designed that had ever actually used a microscope before | 23:14 |
| fenn | i also don't see any X or Y actuation | 23:14 |
| nmz787 | fenn: for laser/DMD litho stuff we wouldn't need a condenser | 23:16 |
| kanzure | fenn: i would prefer not to do a committee | 23:16 |
| kanzure | let's go with a benevolent dictator model | 23:16 |
| kanzure | malevolent dictator also okay | 23:16 |
| fenn | sample lifecam studio output http://fennetic.net/irc/cam1080a.mp4 http://fennetic.net/irc/cam1080b.mp4 from com/shop/usb-microscope-1080p-for-smt-soldering/51-lifecam-studio-1080p-microscope-lens-mod-kit | 23:18 |
| fenn | gah | 23:18 |
| fenn | http://www.diyinhk.com/shop/usb-microscope-1080p-for-smt-soldering/51-lifecam-studio-1080p-microscope-lens-mod-kit.html | 23:19 |
| nmz787 | the benefits of higher framerate for the raspicam are quite a lot i think | 23:19 |
| fenn | too bad the lifecam is rolling shutter, why is everything rolling shutter | 23:20 |
| fenn | nmz787: yeah probably.. i am also just kind of interested in good small hackable webcams | 23:20 |
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| nmz787 | yeah | 23:23 |
| nmz787 | the raspi+cam was $40 when i got it | 23:23 |
| nmz787 | it seemed pretty bad for low-light use, but I never even took the film off the lens so idk how well it was focused/aligned | 23:23 |
| fenn | is it rolling shutter? (wobbly jello effect when shaking) | 23:23 |
| nmz787 | but I imagine enough to do grid reticle stuff | 23:23 |
| nmz787 | yeah I think so | 23:24 |
| nmz787 | pulsed light can get around that | 23:24 |
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| kanzure | in fact, i think the number of designers should be reduced | 23:37 |
| nmz787 | the night is almost over and we didn't spree at all | 23:40 |
| * night nods | 23:40 | |
| fenn | back to my whale watching then | 23:40 |
| kanzure | huh? | 23:40 |
| kanzure | because the design kept changing | 23:41 |
| kanzure | suddenly there are belts | 23:41 |
| kanzure | this is why i am suggesting the number of designers be reduced | 23:41 |
| kanzure | fenn: could you just scribble the rest of it out | 23:41 |
| fenn | i still dont even know what you're building tbh | 23:42 |
| fenn | a laser plotter with micron resolution? | 23:43 |
| kanzure | what is a "plotter" | 23:43 |
| fenn | draws lines | 23:43 |
| kanzure | so, there are a number of techniques for microfabrication that seem to all use the same hardware (other than the write method itself) | 23:43 |
| fenn | exposes film with light | 23:43 |
| nmz787 | you are the only one to mention belts, sir | 23:43 |
| kanzure | you wanted a gear, what are you putting on the gear | 23:43 |
| fenn | you could direct drive the fine focus knob | 23:44 |
| nmz787 | nothing goes on a gear | 23:44 |
| nmz787 | it meshes with adjacent gears | 23:44 |
| kanzure | and what do those adjacent gears mesh to -_- | 23:44 |
| nmz787 | the XY knobs are coaxial kno | 23:44 |
| kanzure | fenn: yes, light of various types: LEDs, laser, LCD projector, DMD projector | 23:44 |
| nmz787 | tho | 23:44 |
| fenn | ok it would seem to be prudent to just use a microscope then, and develop each of these things as a microscope attachment | 23:45 |
| kanzure | also with a camera port | 23:45 |
| nmz787 | they don't mesh to anything else, one gear on the X shaft, on on the Y shaft... one on each of the two stepper motor shafts | 23:45 |
| fenn | unless there is some reason to use all N of them at once | 23:46 |
| nmz787 | find some glue or metal or 3d printed thing, sticks, chewing gum... to mount them so they mesh | 23:46 |
| nmz787 | a motor to an axis-gear | 23:46 |
| kanzure | fenn: camera should be always-on | 23:46 |
| kanzure | fenn: as far as i can tell, the light sources will never be used at the same time, and probably could be switched out if the designer is clever enough with mounts | 23:47 |
| kanzure | where's the spec sheet for which optical mount connectors you need | 23:48 |
| kanzure | for interfacing with the existing microscopes? | 23:49 |
| fenn | michael broxton would know all of this stuff | 23:49 |
| kanzure | and i don't understand why the design is different now | 23:49 |
| kanzure | last time we looked at the laser cutter, it was not in a commodity microscope | 23:49 |
| kanzure | but now it is? | 23:49 |
| fenn | because before you wanted a huge slide with over 9,000 meters of continuous channel | 23:50 |
| kanzure | wasn't it only a few cm? | 23:50 |
| fenn | the specifications were lacking then too | 23:51 |
| fenn | s/slide/microfluidics sandwich/ | 23:51 |
| kanzure | what do you think a microfluidics sandwich is? | 23:51 |
| nmz787 | delicious | 23:51 |
| fenn | the word "slide" is overloaded in this context | 23:51 |
| kanzure | all of the microscope projector lithography things are using "slides" | 23:52 |
| nmz787 | https://www.youtube.com/watch?v=C7HaQucL9pg | 23:52 |
| kanzure | spin coated with photoresist | 23:52 |
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| fenn | i believe nmz787 was pushing for that form factor last(?) year and you wanted something bigger | 23:52 |
| fenn | has anyone seen katsmeow around? | 23:53 |
| kanzure | she appeared once last year | 23:53 |
| nmz787 | i would still love a better than backlash-filled design, but i think we need to get an iteration done with something that is at least accessible | 23:54 |
| kanzure | what the fuck does "accessible" mean | 23:54 |
| fenn | ability to test theories against experiment | 23:54 |
| nmz787 | UPS can deliver it anywhere in the world in 5 to 14 days | 23:55 |
| nmz787 | microscopes and those $3 steppers and gears are accessible | 23:55 |
| kanzure | okay, so what are the new design parameters? | 23:55 |
| nmz787 | cheap is accessible | 23:55 |
| nmz787 | if we do it and it turns out to do 1 micron lines but they're all jerky then we can try a $200 or $400 stage or whatever fenn's thing will cost | 23:56 |
| nmz787 | with the super awesome slides and bearings | 23:56 |
| nmz787 | if the thing gives us 100 micron lines we know | 23:56 |
| nmz787 | maybe it will give 10 micron lines | 23:56 |
| nmz787 | or 20 and be OK with respect to squiglyness | 23:56 |
| kanzure | that sounds a lot like "engineering by not being sure about anything".. | 23:56 |
| nmz787 | we don't know, so lets start with something that some other hacker dudes can easily replicate and augment/respin | 23:57 |
| nmz787 | lets get /some/ data point | 23:57 |
| fenn | yes we should be trying to at least design within an order of magnitude | 23:57 |
| kanzure | or, how about we fucking know things | 23:57 |
| nmz787 | or we're just mentally masturbating | 23:57 |
| kanzure | knowing things is not masturbating... | 23:57 |
| nmz787 | knowing them and talking about dong them someday is | 23:57 |
| nmz787 | i want someday to be yesterday | 23:57 |
| kanzure | you can't just buy random pixie dust and things magically work | 23:57 |
| kanzure | i am so confused | 23:58 |
| nmz787 | and either move on to another project, or come back to it later with a fresh mindset, and in the mean time let it be there for inspiration to others | 23:58 |
| kanzure | so you are opposed to estimation for engineering design, or am i strawmanning you? | 23:58 |
| fenn | i think he is just designing by what's available rather than starting with detailed specs and trying to find the perfect thing | 23:59 |
| nmz787 | .dic strawmanning | 23:59 |
| kanzure | fenn: where "perfect" is "within an order of magnitude" ? | 23:59 |
| nmz787 | .ud strawmanning | 23:59 |
| fenn | strawmanning = putting words in someone's mouth | 23:59 |
| nmz787 | .wik strawmanning | 23:59 |
| yoleaux | "A straw man, also known in the UK as an Aunt Sally, is a common type of argument and is an informal fallacy based on the misrepresentation of the original topic of argument. To be successful, a straw man argument requires that the audience be ignorant or uninformed of the original argument." — http://en.wikipedia.org/wiki/Straw_man | 23:59 |
| --- Log closed Wed Jun 11 00:00:14 2014 | ||
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