2014-06-09.log

--- Log opened Mon Jun 09 00:00:29 2014
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nmz787welp apparently the hackaday raman spectrometer project hasn't actually been tested for signal yet, still cool, gave them some tips00:10
entelechytalking about diy raman spectroscopy?00:18
entelechyhttp://benkrasnow.blogspot.com/2013/05/intro-to-diy-raman-spectroscopy.html00:18
entelechythis guy has done a cool one00:19
nmz787yep00:35
nmz787i talked with him about it at maker faire00:35
nmz787entelechy: specifically I was talking about hackaday.io/project/1279-DIY-3D-Printable-RaspberryPi-Raman-Spectrometer00:35
nmz787it sounds like ben has done better results-wise so far00:36
entelechyyeah he calibrated it and whatnot00:36
entelechyguy works for valve software as their engineer-in-residence00:36
nmz787nice but old digicams seem like they can be found worldwide in grey markets00:36
nmz787rather than 3d printers00:36
nmz787nah google now00:36
nmz787no longer at valve00:36
nmz787i met his dad00:37
nmz787he came up to my booth for takeitapart.com and was telling me how his kid started by taking stuff apart00:37
nmz787and then i asked what he did and if he mentored him and what his kid was doing now00:37
nmz787and he replied he was ham radio guy,( so that set the stage enough for me), then he said his son had a ruby crystal laser at a booth just a few booths down from ours00:38
nmz787and of course i'd already seen it and seen it was ben's booth by that time00:38
nmz787so i knew immediately this was his dad00:38
nmz787it was really cool00:38
nmz787then went and talked to ben for a few minutes00:39
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entelechyah right on01:06
entelechyyeah hes got a bunch of cool videos01:06
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kanzurenmz787: just because it's easy to repurpose stuff you already have doesn't mean you should do it08:50
kanzurenmz787: the idea is to make something repeatable that others can improve on if they choose to08:51
kanzurenmz787: not garbage dive for a one in a trillion part that nobody else will be able to acquire08:51
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kanzurehere's someone that might be selling silver halide film or microfilm stuff: http://www.ilfordphoto.com/aboutus/page.asp?n=2308:56
chris_99ilford make nice produces, i use their 35mm b&w film08:57
chris_99*products08:57
kanzurewhat's the resolution?09:00
chris_99no idea sorry,   the lp/mm or somthing you mean i guess?09:00
kanzureyes09:01
kanzurei was looking at their spec sheet/pdf thing and it doesn't mention it09:01
chris_99hmm must be somewhere09:01
ParahSailinheh, transcriptic wants to talk to me09:25
kanzuretake it and run09:25
kanzurei think they write in scheme09:26
ParahSailinwhere on gnusha do you keep transcripts?09:27
kanzurehttp://diyhpl.us/wiki/transcripts/startup-science-2012/max-hodak/09:29
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nmz787_idingo: around? do you know if wexpect uses a file for pipe file descriptors? i think my problem for stderr getting 'stuck' might have been too large a data without a newline to flush it (though I could be wrong)09:37
dingoaround, not (yet) familiar with expect, but if your child process is writing *a lot* of data, and you are trying to 'child.expect()' something from it, the expect() method will contoniously read (and exaust) the child's stdout/err buffer until it finds it09:46
dingoin a pseudo-terminal (pty) stdout and err (and even stdin) are merged into a single file descriptor. I'm not as certain about wexpect, though.09:47
dingobut if you're not .expect()'ing something, or manually calling .read/.read_nonblocking(), then teh child process will fill its output buffer -- usually 512, 4096, or 65534 bytes, and then block09:47
dingobecause he's calling sys.stderr.write('....') and the OS is blocking this call -- its stuck there09:47
dingotraditionally, in posix, you might be right about stdout -- it is line-buffered, and stderr is unbuffered -- sys.stderr.write('x') is immediately received by the parent process/terminal -- but sys.stdout.write('x') is not, until sys.stdout.flush() or sys.stdout.write('\n newline') happens09:49
dingobut really -- wexpect could be very different in these regards, i have not yet even begun to read its source code, but from the description, it implements an emulated console of its own for win32, so monsters there may be09:49
nmz787_iyeah been reading the source, can't really tell where it's getting its data from... but I got a lead that piping to a file might handle the blocking issue09:56
nmz787_iidk, i'll have to give it a try09:56
kanzure"Although it still supports lxc, docker now defaults to libcontainer ( https://github.com/dotcloud/docker/tree/master/pkg/libcontainer ), it's own container implementation."10:12
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tomkinscpaperbot: http://journals.lww.com/headtraumarehab/Abstract/2005/05000/The_CDC_Traumatic_Brain_Injury_Surveillance.5.aspx10:33
paperbotTypeError: descriptor 'find' requires a 'str' object but received a 'NoneType' (file "/home/bryan/code/paperbot/phenny/modules/scihub.py", line 55, in <lambda>)10:33
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kanzurelike all engineering problems, this can be solved by submerging the whole machine i noil10:41
kanzurelike all engineering problems, this can be solved by submerging the whole machine in oil10:41
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nmz787_ihi tomkinsc!11:02
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kanzurecold shoulder treatment11:22
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kanzurepaperbot: http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=124247012:13
paperbothttp://libgen.org/scimag/get.php?doi=10.1117%2F12.96373412:13
kanzureare these new? http://magzdb.org/ ftp://libgen.org/pictures/ ftp://libgen.org/librusec/ http://libgen.org/biblio/batchsearchindex.php http://dc-poisk.no-ip.org/yndex.html http://dc-poisk.no-ip.org/12:15
kanzurehttp://bookzz.org/ isn't. http://bookfi.org/ i forget if it's the same owner or not. hrm.12:17
kanzureftp://libgen.org/librusec/Librusec/lib.rus.ec/12:18
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kanzure(23 MB) http://liste.polymtl.ca/sympa/d_read/phy-mems/PartageInterne/Books/Rizvi2005HandbookofPhotomaskManufacturingTechnology.pdf12:33
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kanzurekodak still sells microfilm (800 lines per mm, so 1 micron resolution?) http://graphics.kodak.com/docimaging/uploadedFiles/d30.pdf13:13
chris_99what are you planning to use it for?13:15
kanzurephotomask13:15
kanzurereally i think you can just take a picture on normal camera film, shine light through it, and get microstructures...13:16
chris_99a photomask for what sorry?13:16
kanzurestuff, you know13:17
kanzurephotomask for micron-resolution lithography (microelectronics, microfluidics, microwhatever)13:17
chris_99aha13:17
kanzurepaperbot: http://search.proquest.com/docview/27585626813:18
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kanzurethis seems like a cool group, http://www.ime.tsinghua.edu.cn/publish/wdzs/323/index.html13:29
kanzure.title13:29
yoleauxInstitute of Microelectronics, Tsinghua University13:29
gradstudentbotI think the centrifuge is broken.13:29
delinquentmeNot sure if you guys already know about this: https://www.indiegogo.com/projects/vocore-a-coin-sized-linux-computer-with-wifi13:30
delinquentmesuper small linux computer w wifi13:30
chris_99oh yeah i've seen that, looks interesting, it's the MIPS one right13:31
ParahSailinyeah thats the top school there13:32
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kanzurewhy does the us army own patents?13:36
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kanzureParahSailin: i'm trying to find tao deng <dengt@research.ge.com> 518-387-5473 518-387-7548 (emails are bouncing)13:41
gradstudentbotThat's enzymatically impossible.13:44
ParahSailinhadn't thought about this, but snake antivenom is typically a polyclonal ab http://metronews.ca/health/3715/anti-venom-crisis-in-ontario/13:49
kanzure"Layer by layer, the B9Creator uses the light from a Vivitek projector to cure photo-initiated resin rather than extruding plastic. It's similar to the Form1's stereolithography, but can print objects with an XY resolution of 50 microns and a Z resolution of 25 microns."13:52
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kanzurehttps://github.com/lansing-makers-network/buildlog-lasercutter-marlin13:57
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kanzurehttps://www.kickstarter.com/projects/b9creations/b9creator-a-high-resolution-3d-printer/posts/24446014:02
kanzurehmm14:02
kanzureif these machines are really doing micron-resolution stuff, then why are there no microscope images of the work14:02
kanzurehttps://groups.google.com/forum/#!topic/muve-3d-support-group/rv0FJG5TXZU14:03
kanzure"0.0275 mm per step AKA the smallest definable distance the controller can command"14:03
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kanzureso 30 micron steps14:04
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nmz787_ihere's the DMD direct write machine paper showing interpixel photoresist feature noise14:06
nmz787_ihttp://www.intelligentmp.com/Downloads/Technical%20Papers/SF-100%20Greyscale%20Paper.pdf14:06
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nmz787_ithey have lots of other papers on their site too14:06
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kanzurejmil is focusing on large z height dlp printing, apparently14:21
kanzurehe has expressed a disinterest in planar investigations of resolution14:21
kanzurealso he has some photographs of the resolution here http://open3dlp.blogspot.com/2013/09/what-month.html14:21
kanzureugh the dlp dev kit is very inconvienently priced. it means if i buy a few, i'm less likely to run into others that also have it and are willing to test/build with it.14:29
kanzurei wonder what's in the dev kit anyway. just the pcb? or are all of the other micromirror array devices locked down?14:31
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kanzurehm, so, i think it should be kept low-tech: uv/bluray led, projection of laser-printed transparency sheet, dlp stuff would be nice but if others build the device and end up with different projector equipment it will be annoying and intractable14:35
kanzure /win 614:37
kanzurefail14:37
gradstudentbotAre you published?14:37
paperbotRuntimeError: maximum recursion depth exceeded in cmp (file "/usr/lib/python2.7/_weakrefset.py", line 73, in __contains__)14:43
heathhttps://docs.google.com/document/d/17OTxjE5zl34VcXiAORayFOCDIkyRCiefh1ZBN1qEBUc/edit14:44
heathcenter for open science: strategic plan14:44
heath"6. Make all academic research discoverable and accessible"14:45
heath"5. Adjust incentives to make “getting it right” more competitive with “getting it published” "14:46
kanzurethey are lying, they probably only mean the stuff they have access to (for #6)14:46
heath"4. Foster an interdisciplinary community of open source developers, scientists, and organizations."14:46
heathI'm not sure if #3 is possible14:47
kanzurethis is not a plan14:47
heath"3. Join infrastructures to support the entire scientific workflow in a common framework"14:47
heaththey are wanting me to review this and maybe make some suggestions on what possible projects i would work on if i joined them14:48
kanzuremy review would be very negative and scathing14:49
heath:)14:49
kanzuretop-down demands for "organizational synergy" are just not going to do anything14:49
heathI feel like it may be a decent framework for certain typing of researchers, but it seems like it could get in the way of other work14:50
heaths/typing/types14:50
heathiirc after a conversation with someone from there last year, version control to some people is saving a Word document with a new file name14:51
heathand i think this is their target audience right now14:51
kanzurehuh, i didn't know about LCD projectors15:00
kanzurepaperbot: http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=535189015:04
kanzure.title15:04
paperbothttp://libgen.org/scimag/get.php?doi=10.1109%2FMHS.2009.535189015:04
yoleauxDevelopment of the maskless photolithography device with an LCD-projector for fabrication of micropa...15:04
gradstudentbotThe freezer was too cold and fucked up my sample DNA.15:05
kanzurehere it is,15:07
kanzurehttp://diyhpl.us/~bryan/papers2/optics/photolithography/Second-generation%20maskless%20photolithography%20device%20for%20surface%20micropatterning%20and%20microfluidic%20channel%20fabrication%20(using%20an%20LCD%20projector).pdf15:07
kanzure"The fabrication of polyacrylamide (PAAm) micropatterns was performed with a 5x objective lens to adjust the final resolution to 2.5 microns/pixel, and the two-step procedure was employed as described previously.[10]"15:09
kanzure"For the fabrication of PDMS microchannels, a 3x objective lens was employed to adjust the resolution to 5 microns/pixel."15:10
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nmz787_iLCD still has interpixel dead zones15:46
nmz787_iI think the best bet is to trace with a laser15:47
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kanzurenmz787_i: i think the dead zones can be fixed using this method,15:54
kanzurehttp://diyhpl.us/~bryan/papers2/optics/photolithography/Development%20of%20microfabrication%20technology%20with%20maskless%20photolithography%20device%20using%20LCD%20projector%20-%20Itoga%20-%202010.pdf15:54
kanzurebasically just have sub-pixel resolution motion to account for the dead zones15:55
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nmz787_ioh, yeah, sure, sub-pixel movement is gonna be real easy without a nanostepper16:37
nmz787_i:P16:37
nmz787_ii cant read that now16:37
kanzureyou should double check whether or not that actually solves it16:40
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nmz787_ikanzure: well it probably would, but again, now we need some nanostepper17:06
kanzureyou mean to say nanosteppers don't grow on trees?17:08
delinquentmewhat is nanostepper?17:08
kanzureit is a stepper that steps using nm17:08
kanzure*using nm steps17:08
delinquentmeSure I mean the implementation though.  You're just using gearing and a typical stepper right?17:08
kanzurewell that paper used one called "KY1250C-L"17:09
delinquentmehahahah17:09
delinquentmejesus.17:09
kanzure.title http://www.spectracore.com/KY1250CL.html17:09
yoleauxKY1250C-L  Motorized Crossed Roller XY Axis 120x120mm Platform 50mm Travel  Stage17:09
kanzure"Resolution: 0.05micrometer(1/20)"17:09
delinquentmeEhh itll work.17:09
kanzure50 nm step17:10
delinquentmeyeah its using gear boxes ... And its certainly pretty17:10
delinquentmeBut the connectors just scream "markup"17:10
delinquentmeY no 4 or 8 pin connections?17:10
kanzurewho knows, i'm just quoting what the paper said17:12
delinquentmeI'd guess they also sell just the mechanical stage17:12
delinquentmeand depending on the application that could be easier if you just slap your own steppers in on it17:13
kanzurefenn's laser cutter design is 1.5875 microns per step17:13
delinquentmeThe biodome: http://www.ncbi.nlm.nih.gov/pubmed/2070895617:14
delinquentmedude. fucking pig bladders17:15
delinquentmewe throw that shit on EVERYTHING.  Humans, horses , mice17:15
kanzureugh "Since 2005,[7] the only remaining manufacturers of the LCDs for LCD projectors are Japanese imaging companies Epson and Sony."17:22
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kanzureoh, "According to electronics industry research company Pacific Media Associates, projectors using 3LCD technology comprised about 51% of the world's digital projector market in 2009.[2]"17:24
kanzure.wik liquid crystal on silicon17:25
yoleaux"Liquid crystal on silicon (LCoS or LCOS) is a "micro-display" technology developed initially for projection televisions but now used also in Wavelength Selective Switches, structured illumination and Near-eye displays." — http://en.wikipedia.org/wiki/Liquid_crystal_on_silicon17:25
kanzuredid not know this "Texas Instruments' DLP (Digital Light Processing) relies on a spinning color wheel to reproduce images"17:29
kanzuremakes sense though, since the mirrors need to reflect something17:29
kanzurei can't tell if that means lcd projectors are dying or not17:32
chris_99laser projectors seem a cool idea to me17:32
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kanzurenmz787_i: so, the one reason to go with the LCD method is that the pixels are already pretty small. you only need a 2-5x objective as opposed to 100x plus oil immersion or w/e.18:47
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nmz787_ikanzure: but i'm saying get away from pixels altogether20:00
kanzureisn't a laser beam just a non-square pixel20:01
nmz787_ikanzure: binocular microscope, video in one ocular, laser in the other, bluray next to the objective too (so two write methods and a read method)... then have a laser printed grid of lines under the objective, use fast video camera to feedback for motion control of the stage and absolute positioning20:01
nmz787_iwell except that when you drag it it, well, drags20:02
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nmz787_iso if the drag operation is relatively smooth, there is less interpixel noise20:02
nmz787_ifenn would say something about inertia smoothing things20:02
kanzurecannibalizing a microscope isn't a good idea- we should just buy the objectives and put it on the frame ourselves20:03
nmz787_iso maybe video would only be needed to calibrate once, in case of any large leadscrew errors or something20:03
nmz787_ior to watch for backlash20:03
nmz787_ia microscope is a microscope, i said nothing about cannibalizing there20:03
nmz787_iit will be harder to make a bino microscope though20:04
nmz787_iit would be much easier to outsource to some factory in china, my time is already pretty limited now20:04
kanzurewhy do you want binocular20:04
nmz787_iso you can have video and laser20:04
kanzuremost people mean the eye-level thing when they say binocular20:04
nmz787_ino20:04
nmz787_iwell20:05
nmz787_ii mean, yeah, there's a beamsplitter20:05
nmz787_ithat has been hopefully finely and well adjusted20:05
nmz787_i(i used the word ocular, which is the eyepiece lense unit)20:05
kanzure"cannibalizing" means buying an existing microsocpe, removing its stage and replacing it with ours, etc.20:05
nmz787_ithey might sell us a scope cheaper if we didnt want the stage20:06
nmz787_iidk20:06
kanzureand what's with the weirdo curved neck they all have, ugh20:06
nmz787_iwhy does it matter?20:07
nmz787_iyou want it hooked up to internet anyway20:07
nmz787_i:/20:07
nmz787_idoes jules have any time?20:07
kanzurewhat does jules have to do with it?20:08
kanzureit matters because project repeatability20:08
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kanzurewhat's so bad about building a frame anyway20:08
kanzureyou get to put everything where you need it instead of where it happens to be20:09
nmz787_ijules is pretty god with optics20:09
nmz787_iand he's local so that makes physical collab easier for a hardware project20:09
kanzurei think this is going to end up being like a single objective20:10
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nmz787_iright20:13
kanzurewith the trifocal microscopes part of the problem is mounting your other equipment on that third ocular20:14
kanzurewith your own design, you could make something more sane that isn't putting its weight on that vertical tube20:14
nmz787_itrinocular20:15
kanzureoh right20:15
kanzurenot trifocal20:15
nmz787_ii said bino earlier20:15
nmz787_iFWIW the trinocular mounts are usually quite solid20:15
nmz787_imounting onto the oculars is much more of a head-scratcher for me20:16
nmz787_ibeacuse they're absolutely not made to be attached to20:16
nmz787_ii'd like you to find someone to improve that openlabtools CAD20:16
kanzurethat just seems silly to me- i can't think of a situation where i wouldn't want to be able to attach things20:16
kanzureyou mean someone to redo it?20:17
nmz787_iyeah and do any additions20:17
kanzurei was thinking of redoing them myself since i didn't like stl20:17
nmz787_iI'm not too quick with CAD stuff20:17
nmz787_iat least not the 3d printed stuff20:17
nmz787_iis that how you'd want this to be done, 3d printed?20:17
kanzureoof, i haven't thought about it20:18
kanzureis there any reason to go one way or the other20:18
kanzurebesides cost20:19
nmz787_istructure, how much weight it can support20:19
nmz787_iflexibility20:19
nmz787_idon't want it twisting around and deforming with stress20:19
nmz787_igoing out of calibration20:19
nmz787_iwhatever that may or may not consist of20:19
kanzureoh right, weight.. let's estimate a projector is 5 kg at most20:20
nmz787_ii was planning on microstepping geared stepper motors20:20
nmz787_ithere would be backlash20:20
nmz787_ibut i think it should be pretty dang smooth travel20:20
nmz787_i(also I already have a working DMD with the light removed and have shined a laser into to get an image successfully)20:21
nmz787_ii found a decent laser seller on aliexpress20:21
nmz787_ibasically a 405nm laser with a metal heatsink and adjustable glass focus lens20:22
nmz787_ilike $40 i think20:22
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nmz787_iI never ordered it tho20:22
kanzurethe gearbox stepper you wanted was NEMA 17?20:23
kanzureoh you can turn a NEMA 17 into a screw actuator20:34
kanzure.title http://www.pololu.com/product/226820:35
yoleauxStepper Motor with 28cm Lead Screw: Bipolar, 200 Steps/Rev, 42×38mm, 2.8V, 1.7 A/Phase20:35
kanzure"The nut moves 8.0 mm per full revolution of the lead screw, which allows for a linear resolution of 0.040 mm per full step of the stepper motor. Even smaller step sizes can be achieved through microstepping, which is a feature of many bipolar stepper motor drivers. We recommend the DRV8825 stepper motor driver carrier for use with this stepper motor, which allows for a linear resolution of 1.25 µm per 1/32 microstep. However, please note ...20:36
kanzure... that the nut is not spring loaded, so changes in direction will result in loss of positioning precision due to backlash."20:36
kanzurewould moving forward more than you need be sufficient to eat the backlash?20:44
kanzureor would the microstepping still be off20:44
nmz787_iyeah you have to compensate for backlash20:49
nmz787_iwhich is why i was thinking live video of a grid reticle (laser printed checkerboard)20:49
nmz787_iblob tracking20:50
nmz787_iwhether live or mostly calibration, idk yet20:50
nmz787_ii was thinking these to start out with, if it was just a microscope slide or piece of spin-coated silicon/glass http://robocraft.ru/files/datasheet/28BYJ-48.pdf20:52
nmz787_ii already have them microstepping with PWM with a 128 point sine lookup table20:53
kanzure.title http://liutaiomottola.com/Tools/Backlash.htm20:53
yoleauxBacklash in Lead Screws: What It is and What to do About It20:53
nmz787_ifor an attempt to increase smoothness20:53
kanzureit mentions a software fix which is exactly my "eat the backlash" method.. so whatever.20:53
nmz787_ithose motors are apparently from auto HVAC vent controls20:54
nmz787_iwith a driver board and wires and connectors they're like $3 or $420:54
kanzureis that a 5.6 degree stepping angle?20:54
nmz787_iits less than 1 since its geared, then with the microstepping even more21:05
nmz787_imicrostepping is basically free for smoothing the power out, but with all the gears and such, you need to do all the positioning based off the home/center point21:06
nmz787_iyou can't say 50 microsteps to  the right is 5 microns21:06
nmz787_iyou'd need to ask how many microsteps is it to get 5 microns, from the calibration data, to know at that point on the stage, how many microsteps it will take to travel21:07
kanzureyep21:07
nmz787_iso again, the video21:07
kanzurewould be nice to have a scalable number of oculars, based on adding mirrors or whatever21:09
nmz787_ikanzure: i guess you could start working from fenn's model, and redo the openlabtools augmentation21:09
kanzureaugmentation?21:09
nmz787_ii think it might just be another of fenn's model rotated and added on21:09
nmz787_iwell for the Z21:09
nmz787_ii dont remember how far along his model was21:09
nmz787_ithat's why infinity corrected objectives are nice21:10
nmz787_ithe only req is a 'tube lens'21:10
nmz787_iwhich I asked about here https://github.com/OpenLabTools/Microscope/issues/221:10
nmz787_ii bought a plano convex or two from ebay a while ago that were unused nice edmunds or thorlabs surplus21:11
nmz787_iI think it could probably be a smaller diameter21:12
nmz787_iand idk where a good new source is21:12
kanzure"Yes, sorry for the disorganised state of our wiki, with 5 people working on the project for 10 weeks we spent most of the time building and not enough time organising our work."21:14
kanzurewhy so many people??21:14
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kanzureneat, there are gigahertz-range rf microfluidic antennas built with liquid metal21:43
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kanzure.title http://www.microfluidics.iis.u-tokyo.ac.jp/r09001.html22:09
yoleauxEO pump-based system22:09
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kanzure"This study reports the development of a prototype sheet-like soft actuator named a "microhydraulic actuator", which creates a 3D motion from a planar body with 2D fluidic channel patterns (Fig. A). In our proposed microhydraulic system, the miniaturized electroosmotic pumps (EOPs) as the pressure generating devices are embedded into the sheet-like body of the actuator for integration, miniaturization and low-power-consumption of the total ...22:11
kanzure... system." http://www.microfluidics.iis.u-tokyo.ac.jp/r13013.html22:11
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kanzuremicrofluidic pump array instead of using a bunch of external syringe pumps http://www.microfluidics.iis.u-tokyo.ac.jp/r10001.html22:14
kanzureparticle sorting by using surface relief structures http://www.microfluidics.iis.u-tokyo.ac.jp/r08004.html22:18
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kanzureyeesh this is a bulky microscope http://www.zeiss.com/microscopy/en_de/products/light-microscopes/axio-imager-2-for-biology.html23:02
kanzuremulti-ocular microscope http://www.microscopesmanufacturer.com/product/COAXIAL%20MICROSCOPES/HL-54.jpg23:11
kanzuregeeze they sell that for $9k? http://www.ebay.com/itm/Accu-Scope-3025-5-Head-Multi-Viewing-Observation-Teaching-Microscope-New-/261491632472?pt=LH_DefaultDomain_0&hash=item3ce21da95823:15
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kanzureTodh5als: hi23:43
Todh5alshi, kanzure23:45
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