Paper request
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Sebastian S Cocioba
Dec 27, 2014, 4:08:28 AM12/27/14
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"Culture and chemical-induced fusion of tobacco mesophyll protoplasts in a microfluidic device"
If anyone has access to this article and is willing to share, please let me know. Thanks!
Sent from my iPad
Sent from my iPad
Dakota Hamill
Dec 27, 2014, 6:01:43 AM12/27/14
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You're up early, putting in work!
I tried a few databases from my school proxy but none had that book. I find chapters in books I have a 10% or less success rate with as compared to journal articles.
That I thought was close, different name, but many of the same authors and seems to be on the same or related topic.
Could try full text request from this guy.
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scoc...@gmail.com
Dec 27, 2014, 6:10:24 AM12/27/14
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Tom's link worked perfectly. Thanks for the effort Dakota! Gonna see how small of a feature I can shrinky dink. I was planning some circuit like this last year but never got around to it. Worried the 20um posts will be too difficult to print and shrink properly. Even at the shrink rate of 63% (cited in shrinkydink microfluidics paper) I'd still need around 40um initial features so well see. Worst case maybe a series of smaller and smaller pillars. I'll post files once I get comfy with draftsight and thing actually works.
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D
From: Dakota Hamill
Sent: 12/27/2014 6:01 AM
To: diy...@googlegroups.com
Subject: Re: [DIYbio] Paper request
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CAGdeWmSGG1RV2cV%3Drw-f1sjn4OvX4eGnyFAuLDE64vJWkOTp4g%40mail.gmail.com.
Nathan McCorkle
Dec 27, 2014, 10:46:23 PM12/27/14
to diybio
On Sat, Dec 27, 2014 at 3:09 AM, <scoc...@gmail.com> wrote:
> Tom's link worked perfectly. Thanks for the effort Dakota! Gonna see how
> small of a feature I can shrinky dink. I was planning some circuit like this
> last year but never got around to it. Worried the 20um posts will be too
> difficult to print and shrink properly. Even at the shrink rate of 63%
> (cited in shrinkydink microfluidics paper) I'd still need around 40um
> initial features so well see. Worst case maybe a series of smaller and
> smaller pillars. I'll post files once I get comfy with draftsight and thing
> actually works.
>
I just bought this yesterday for exposing photoresist, to use for
> Tom's link worked perfectly. Thanks for the effort Dakota! Gonna see how
> small of a feature I can shrinky dink. I was planning some circuit like this
> last year but never got around to it. Worried the 20um posts will be too
> difficult to print and shrink properly. Even at the shrink rate of 63%
> (cited in shrinkydink microfluidics paper) I'd still need around 40um
> initial features so well see. Worst case maybe a series of smaller and
> smaller pillars. I'll post files once I get comfy with draftsight and thing
> actually works.
>
imprinting silicone, or maybe for use as a lithography photomask.
http://www.ebay.com/itm/Mini-Laser-200-250mW-Engraving-Machine-DIY-Carving-Logo-Picture-Marking-Printer/261591526091
The ebay listing says it is accurate to 10 microns, but I doubt the
laser spot will even be that small. Also I am not sure if that number
is realistic or just made up... but the stepper controller does have
microstepping so I have hope. I have a few ideas for upgrading the
laser, basically just adding a tube to hold the laser unit from a
blu-ray drive (because the optics in that have tons and tons of
engineering behind them to make them near perfect), or adding better
lenses and a pinhole in an optical tube.
Also it uses open-source hardware which is pretty cool, and I think
this is the relevant line of code to set the resolution of the
software:
https://github.com/grbl/grbl/blob/615093ccd2a9bd63f1ecd29c464f032000f5e626/defaults.h#L50
I recently made this in implicitCAD, I haven't made anything else
yet... but I will give your fluidic a shot!
https://github.com/nmz787/microfluidic-cad/blob/master/implicitCAD/output/sinusoidal_mixer.png
scoc...@gmail.com
Dec 28, 2014, 1:22:00 PM12/28/14
to diy...@googlegroups.com
Looks like a nice little laser set. I have the cheapo china 40w blue and white laser cutter but not sure mirror and lenses are aligned. Still need to find some time to set it up.
What kind of photoresist do you use? I saw that blue dry film thing on eBay but I'm skeptical. I have a UV sterilizer bread-box so exposing it should work. Getting a hold of SU-8 seems tricky especially with all the viscosities available. Would also need to make a wafer spinner or hack a microcentrifuge sans rotor from one of those super cheap offers on eBay to hold a suction cup....i don't trust myself with making one diy and keeping it balanced at high speeds. Also with SU-8 you need a bunch of extra stuff to silanize the water so it doesn't stick to the pdms and the etchant and whatnot. At the same time you only need to make one master and you'll be set for many many recasts. Currently in trying to get a decent vacuum in my hacked Pyrex bottle to spark an oxygen plasma for treating the pdms and glass slide. Know how long the hydrophilic silanol groups last? Any means of storing?
What kind of photoresist do you use? I saw that blue dry film thing on eBay but I'm skeptical. I have a UV sterilizer bread-box so exposing it should work. Getting a hold of SU-8 seems tricky especially with all the viscosities available. Would also need to make a wafer spinner or hack a microcentrifuge sans rotor from one of those super cheap offers on eBay to hold a suction cup....i don't trust myself with making one diy and keeping it balanced at high speeds. Also with SU-8 you need a bunch of extra stuff to silanize the water so it doesn't stick to the pdms and the etchant and whatnot. At the same time you only need to make one master and you'll be set for many many recasts. Currently in trying to get a decent vacuum in my hacked Pyrex bottle to spark an oxygen plasma for treating the pdms and glass slide. Know how long the hydrophilic silanol groups last? Any means of storing?
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D
Subject: Re: [DIYbio] Paper request
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Nathan McCorkle
Dec 28, 2014, 11:30:09 PM12/28/14
to diybio
On Sun, Dec 28, 2014 at 10:21 AM, <scoc...@gmail.com> wrote:
> Looks like a nice little laser set. I have the cheapo china 40w blue and
> white laser cutter but not sure mirror and lenses are aligned. Still need to
> find some time to set it up.
You want to get a square of liquid crystal, like a mood ring, since it
> Looks like a nice little laser set. I have the cheapo china 40w blue and
> white laser cutter but not sure mirror and lenses are aligned. Still need to
> find some time to set it up.
changes color when the CO2 laser heats it up. MUCH easier than reusing
old thermal receipt paper.
http://www.amazon.com/American-Science-Surplus-Liquid-Crystal/dp/B002V05RWI/ref=sr_1_3?ie=UTF8&qid=1419823528&sr=8-3&keywords=liquid+crystal
>
> What kind of photoresist do you use?
> I saw that blue dry film thing on eBay
> but I'm skeptical.
check out his youtube videos for a quick overview.
> I have a UV sterilizer bread-box so exposing it should
> work.
find a decent way to make. Projectors are one way, but the CNC UV
laser seems like it should be decent to get started and the general
idea is super-hackable. There are tons of XY gantry from trash
instructables.
> Getting a hold of SU-8 seems tricky especially with all the
> viscosities available.
SU-8 is that it has better aspect-ratio, or how steep the sidewalls
can end up as a limitation of the photoresist alone (i.e. with a
really nice tight spot and focus and depth-of-field through the entire
film thickness). This might not matter at all with large enough
channels (at a certain point you have to think about channel collapse)
and a lot of the valving techniques actually require or can tolerate
some parabolic/curved profile.
> Would also need to make a wafer spinner or hack a
> microcentrifuge sans rotor from one of those super cheap offers on eBay to
> hold a suction cup....i don't trust myself with making one diy and keeping
> it balanced at high speeds.
vacuum bearings, but I haven't had the time and neither the machining
experience. I am just now getting started with CAD use pretty much,
but also a lab I have access to now has a decent professional
spin-coater.
> Also with SU-8 you need a bunch of extra stuff
> to silanize the water so it doesn't stick to the pdms and the etchant and
> whatnot.
how carefully you peel it, how long it cured for and the temps of
that. Folks in the 3D printing arena actually use PDMS for
anti-stiction of their 3D printing stages! I've been looking and
asking for a while online about the even less-sticky varieties, to
basically no answer.
From checking some things just now, it seems that some people use PDMS
on the photoresist, then peel and coat the PDMS with anti-stiction,
then pour more PDMS and peel the two PDMS apart along the
anti-stiction layer.
http://diyhpl.us/~nmz787/pdf/Anti-stiction_coating_of_PDMS_moulds_for_rapid_microchannel_fabrication_by_double_replica_moulding.pdf
From checking sigma for fluro-silanes, it seems this stuff is know to
work and is $73 for 10g... not great but not horrible either I guess,
relative to the other prices on other known-to-work fluorosilanes:
http://www.sigmaaldrich.com/catalog/product/aldrich/448931?lang=en®ion=US
There is also a chance that the never-wet spray-can stuff you might
find at a wal-mart or hardware store may work... that is just
speculation though.
I'll probably expose the photoresist, cure, add PDMS, cure try
peeling, then expose to plasma for a while to hope to ash any
organics from the non-silica-based-photoresist. Then I'll throw down
some $ for anti-stiction. I'll probably also try using photoresist
itself, though I wouldn't trust that for any reactions... just for
proving the exposure and alignment of the system (and use pretty food
coloring).
> At the same time you only need to make one master and you'll be set
> for many many recasts. Currently in trying to get a decent vacuum in my
> hacked Pyrex bottle to spark an oxygen plasma for treating the pdms and
> glass slide. Know how long the hydrophilic silanol groups last? Any means of
> storing?
plasma bonder using a home microwave, vacuum pump, small oxygen
cylinder, a section of 6 inch PVC pipe, gaskets, gas valves, and flat
end pieces.
Have you seen this?:
http://www.youtube.com/watch?v=N-R0_nXpc7I
-Nathan
Nathan McCorkle
Dec 28, 2014, 11:34:22 PM12/28/14
to diybio
On Sun, Dec 28, 2014 at 8:29 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
> From checking sigma for fluro-silanes, it seems this stuff is know to
> work
Here is that reference:
> From checking sigma for fluro-silanes, it seems this stuff is know to
> work
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3364836/
Nathan McCorkle
Dec 28, 2014, 11:46:17 PM12/28/14
to diybio
On Sat, Dec 27, 2014 at 7:45 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
> I recently made this in implicitCAD, I haven't made anything else
> yet... but I will give your fluidic a shot!
> https://github.com/nmz787/microfluidic-cad/blob/master/implicitCAD/output/sinusoidal_mixer.png
I pooled the papers together that the fabrication steps refer to when
> I recently made this in implicitCAD, I haven't made anything else
> yet... but I will give your fluidic a shot!
> https://github.com/nmz787/microfluidic-cad/blob/master/implicitCAD/output/sinusoidal_mixer.png
talking about the symmetrical birfurcation for dispersion (which the
references don't mention, at least using those keywords):
diyhpl.us/~nmz787/pdf/Microfabricated_arrays_for_high-throughput_screening_of_cellular_response.pdf
http://diyhpl.us/~nmz787/pdf/Versatile_fully_automated_microfluidic_cell_culture_system.pdf
http://diyhpl.us/~nmz787/pdf/Dynamic_single_cell_culture_array.pdf
And the original:
http://diyhpl.us/~nmz787/pdf/Culture_and_chemical-induced_fusion_of_tobacco_mesophyll_protoplasts_in_a_microfluidic_device.pdf
My progress since yesterday:
https://raw.githubusercontent.com/nmz787/microfluidic-cad/master/implicitCAD/output/tobacco_mesophyll_protoplast_fusion_device.jpg
(for some reason it doesn't render for me unless I download it then
open it in my browser, or inkscape)
https://raw.githubusercontent.com/nmz787/microfluidic-cad/master/implicitCAD/output/tobacco_mesophyll_protoplast_fusion_device.svg
https://raw.githubusercontent.com/nmz787/microfluidic-cad/master/implicitCAD/output/tobacco_mesophyll_protoplast_fusion_device__3D.png
and the source code:
https://github.com/nmz787/microfluidic-cad/blob/master/implicitCAD/tobacco_mesophyll_protoplast_fusion_device.escad
I am new to using this CAD software, and I am not sure it is something
I want to continue using or not... as you can see the JPG (which is a
snapshot of an SVG file the CAD tool generated) is not perfect around
the posts (not to mention I didn't finish the end of the channel
exactly as the paper did). I think I can turn up the $quality
variable, which makes rendering take a bit longer but might fix the
weird looking posts completely. I think the CAD tool can emit gcode,
which the UV laser engraver can take as input... so I guess I have to
investigate a g-code viewer to make sure it looks OK before exposing
some resist.
I think the CAD code should be easily ported to other CAD tools like
openSCAD or freecad, but I haven't made any progress with them as
easily as I have with this implicitCAD so far. More to learn and play
with!
Nathan McCorkle
Dec 28, 2014, 11:47:57 PM12/28/14
to diybio
On Sun, Dec 28, 2014 at 8:45 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
> https://raw.githubusercontent.com/nmz787/microfluidic-cad/master/implicitCAD/output/tobacco_mesophyll_protoplast_fusion_device.jpg
and yeah I know I need to improve the funnel-of-posts angle so the
edges follow the pitch of the posts, so i.e. cells don't get stuck.
> https://raw.githubusercontent.com/nmz787/microfluidic-cad/master/implicitCAD/output/tobacco_mesophyll_protoplast_fusion_device.jpg
and yeah I know I need to improve the funnel-of-posts angle so the
edges follow the pitch of the posts, so i.e. cells don't get stuck.
Nathan McCorkle
Dec 29, 2014, 3:21:44 AM12/29/14
to diybio
https://www.youtube.com/watch?v=03tx4v0i7MA
--
-Nathan
scoc...@gmail.com
Dec 29, 2014, 6:26:48 PM12/29/14
to diy...@googlegroups.com
At the moment, my main strife is with my vacuum pump. Its a single stage that can kinda almost not really go to 29"Hg. The MIT nanomaker video on pdms oxidation via microwave oxygen plasma said we need to pull a vacuum of 6 torr or less (<29.8inHg) I don't really trust my vacuum gauge but after some fitting tightening and Teflon taping, I got it to go to 29"Hg. Most two stage pumps state they can down to 6 torr but I really don't feel like buying another pump albeit for the low price of $114.
I went to Brooklyn Glass a while back and the neon guy showed me air plasma in a neon tube but I forgot what pressure he pulled. The experiment here:
https://m.youtube.com/watch?v=fMUemBZ0k5Q
Is so simple but a few setbacks have made me a bit frustrated. The two all-plastic vales I installed into my Pyrex bottle cap had some fun quirks. That ended up causing a leak. I fixed that problem with some JB Weld but now it seems my vacuum pump can't pull low enough. I found a corona treater on eBay for cheap but only has the needle probe not the wide angle spreader. Worst case ill try that. Also found an interesting article on UV based pdms oxidation via ozone but its paywalled for me:
http://www.sciencedirect.com/science/article/pii/S0925400503007482
I'm getting the hang of draftsight but I don't trust the hatching it does to fill in the spaces to make a printable negative. It does a "low-poly" type fill that leaves these secant gaps around curves which may interfere with the channels. I guess I could just reflow the toner ink. I'm using shrinkydinks at the moment....
Why is it so complex to make simple shapes using CAD programs?!?! I actually found LibreCAD to be quicker to use. Seems like it has the same functionality and works fine for building fluidics. Just make sure to use closed polylines, not lines, and join them as you go. Kinda like compiling code often to avoid bugs later on.
In DraftSight, once u lay a polyline, just right click and hit arc to make curves. I always snap to grid and Ortho since my first circuits are just gradient generators and are more or less square with the grid. If the arc doesn't form in the direction you want, just right click and hit direction and draw a line in the direction you want and that should fix the arc issue. Once your chip circuit is done, highlight all the points and right click, editPolyline, type join, hit enter. That should make everything one big polygon if all is closed.
I went to Brooklyn Glass a while back and the neon guy showed me air plasma in a neon tube but I forgot what pressure he pulled. The experiment here:
https://m.youtube.com/watch?v=fMUemBZ0k5Q
Is so simple but a few setbacks have made me a bit frustrated. The two all-plastic vales I installed into my Pyrex bottle cap had some fun quirks. That ended up causing a leak. I fixed that problem with some JB Weld but now it seems my vacuum pump can't pull low enough. I found a corona treater on eBay for cheap but only has the needle probe not the wide angle spreader. Worst case ill try that. Also found an interesting article on UV based pdms oxidation via ozone but its paywalled for me:
http://www.sciencedirect.com/science/article/pii/S0925400503007482
I'm getting the hang of draftsight but I don't trust the hatching it does to fill in the spaces to make a printable negative. It does a "low-poly" type fill that leaves these secant gaps around curves which may interfere with the channels. I guess I could just reflow the toner ink. I'm using shrinkydinks at the moment....
Why is it so complex to make simple shapes using CAD programs?!?! I actually found LibreCAD to be quicker to use. Seems like it has the same functionality and works fine for building fluidics. Just make sure to use closed polylines, not lines, and join them as you go. Kinda like compiling code often to avoid bugs later on.
In DraftSight, once u lay a polyline, just right click and hit arc to make curves. I always snap to grid and Ortho since my first circuits are just gradient generators and are more or less square with the grid. If the arc doesn't form in the direction you want, just right click and hit direction and draw a line in the direction you want and that should fix the arc issue. Once your chip circuit is done, highlight all the points and right click, editPolyline, type join, hit enter. That should make everything one big polygon if all is closed.
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D
From: Nathan McCorkle
Sent: 12/29/2014 3:21 AM
To: diybio
Subject: Re: Microfluidics Chat Thread WAS: [DIYbio] Paper request
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scoc...@gmail.com
Dec 30, 2014, 11:29:54 PM12/30/14
to diy...@googlegroups.com
See attached photo for an example of my crappy attempt at making pdms more hydrophilic using a UV sterilizer (the breadbox type). 30 minute exposure on both a piranha-treated microscope slide (15min in a solution of 3:1 h2so4:h2o2 *dangerous, corrosive, always use appropriate PPE*) and a freshly minted pdms chip. I dried the slide with a kimwipe and used scotch tape to remove residual dust from the feature side of the pdms chip. Then I just laid the slide and pdms chip (feature side up) into the chamber and set a timer for 30 minutes. Then quickly place the pdms chip feature side down onto the slide and apply gentle pressure around the features. Be sure to not squash the channels.
PDMS was the knock-off ML Solar brand from eBay. 10:1 mix by weight. Degassed in a desiccation chamber to 25+inHg twice and incubated at 60c for 1hr.
Pdms chip was casted in a plastic Petri dish on a shrunk shrinky dink printed using graffix brand shrinkable sheet (white not clear!). Something funky about the clear version. Sticks to everything when in the oven, got better results with white sheets. Printed with a standard brother monochrome laser printer (toner). Chip design taken from template PowerPoint slide from this site:
http://chemistry.beloit.edu/Edetc/nanolab/shrink/index.html
Its a simple gradient generator. Still not as fluid and wettable as I'd like it to be. I used a straw to mouth-vacuum from the outlet port. Aside from some funky phenomena on the rightmost channel, it did seem to separate decently. I used food coloring as the indicator.
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D
Sent: 12/29/2014 3:21 AM
To: diybio
Subject: Re: Microfluidics Chat Thread WAS: [DIYbio] Paper request
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Cathal (Phone)
Dec 31, 2014, 4:22:18 AM12/31/14
to diy...@googlegroups.com
Ah Sebastian, you rock. Thanks for the rigorous and methodical write-up. :)
On 31 December 2014 04:29:17 GMT+00:00, scoc...@gmail.com wrote:
See attached photo for an example of my crappy attempt at making pdms more hydrophilic using a UV sterilizer (the breadbox type). 30 minute exposure on both a piranha-treated microscope slide (15min in a solution of 3:1 h2so4:h2o2 *dangerous, corrosive, always use appropriate PPE*) and a freshly minted pdms chip. I dried the slide with a kimwipe and used scotch tape to remove residual dust from the feature side of the pdms chip. Then I just laid the slide and pdms chip (feature side up) into the chamber and set a timer for 30 minutes. Then quickly place the pdms chip feature side down onto the slide and apply gentle pressure around the features. Be sure to not squash the channels.
PDMS was the knock-off ML Solar brand from eBay. 10:1 mix by weight. Degassed in a desiccation chamber to 25+inHg twice and incubated at 60c for 1hr.
Pdms chip was casted in a plastic Petri dish on a shrunk shrinky dink printed using graffix brand shrinkable sheet (white not clear!). Something funky about the clear version. Sticks to everything when in the oven, got better results with white sheets. Printed with a standard brother monochrome laser printer (toner). Chip design taken from template PowerPoint slide from this site:
http://chemistry.beloit.edu/Edetc/nanolab/shrink/index.html
Its a simple gradient generator. Still not as fluid and wettable as I'd like it to be. I used a straw to mouth-vacuum from the outlet port. Aside from some funky phenomena on the rightmost channel, it did seem to separate decently. I used food coloring as the indicator.
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&DOn Sun, Dec 28, 2014 at 8:47 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
From: Nathan McCorkle
Sent: 12/29/2014 3:21 AM
To: diybio
Subject: Re: Microfluidics Chat Thread WAS: [DIYbio] Paper request
> On Sun, Dec 28, 2014 at 8:45 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
>> https://raw.githubusercontent.com/nmz787/microfluidic-cad/master/implicitCAD/output/tobacco_mesophyll_protoplast_fusion_device.jpg
>
> and yeah I know I need to improve the funnel-of-posts angle so the
> edges follow the pitch of the posts, so i.e. cells don't get stuck.
Which is demonstrated on the macroscale with marbles:
https://www.youtube.com/watch?v=03tx4v0i7MA
--
Sent from my Android device with K-9 Mail. Please excuse my brevity.
scoc...@gmail.com
Jan 4, 2015, 7:23:51 PM1/4/15
to diy...@googlegroups.com
So I really can't find an easy way to make circuit designs. I tried libreCAD, DraftSight, and inkscape and it seems that scale and simple shapes is really annoying to do. I'm about to either draw it by hand with epoxy and a needle tip dispenser or use MS Paint. This is just silly. Either in being silly and missing some crucial step or, through the sheer complexity of the programs, simple geometries are not so intuitive to draw. Anyone have a favorite tool and is willing to post a tutorial on how to use it for making microfluidic circuits? Else ill just go through the myriad draftsight tutorials and post one once I tame this beast. Thanks!
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D
Sent: 12/29/2014 3:21 AM
To: diybio
Subject: Re: Microfluidics Chat Thread WAS: [DIYbio] Paper request
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Nathan McCorkle
Jan 4, 2015, 8:09:49 PM1/4/15
to diybio
So far I've had the most 'success' using implicitCAD (to make that
mesophyll protoplast fusion chamber), it can export as STL or SVG if
you don't do any 3D (i.e. extrude) operations, with arbitrary quality
(higher quality means it does more mathematical calculations to refine
the rendered output). 2D rendering is much faster than STL.
I also have been playing with verbnurbs, but have only made a
parametric parabolic channel, and it currently doesn't have data
export... though people tell me since it has triangles already
(tesselation generates triangles from the 3D math operations) it is
relatively easy to implement STL export... which could then be sent to
any existing STL slicing program to get lithography masks (or in the
case of laser-printer + shrinky-dink, deposition traces).
http://nmz787.github.io/html/microfluidics_cad.html
(Sometimes it seems I have to refresh that page to get dragging and
zooming and panning to work)
> https://groups.google.com/d/msgid/diybio/54a9d993.105f8c0a.8796.ffff9c16%40mx.google.com.
--
-Nathan
mesophyll protoplast fusion chamber), it can export as STL or SVG if
you don't do any 3D (i.e. extrude) operations, with arbitrary quality
(higher quality means it does more mathematical calculations to refine
the rendered output). 2D rendering is much faster than STL.
I also have been playing with verbnurbs, but have only made a
parametric parabolic channel, and it currently doesn't have data
export... though people tell me since it has triangles already
(tesselation generates triangles from the 3D math operations) it is
relatively easy to implement STL export... which could then be sent to
any existing STL slicing program to get lithography masks (or in the
case of laser-printer + shrinky-dink, deposition traces).
http://nmz787.github.io/html/microfluidics_cad.html
(Sometimes it seems I have to refresh that page to get dragging and
zooming and panning to work)
--
-Nathan
John Griessen
Jan 5, 2015, 3:17:25 PM1/5/15
to diy...@googlegroups.com
On 01/04/2015 06:23 PM, scoc...@gmail.com wrote:
> Anyone have a favorite tool and is willing to post a tutorial on how to use it for making microfluidic circuits?
Not exactly, but FreeCAD is likely up to it. Would be happy to do a test draw in parallel with you
> Anyone have a favorite tool and is willing to post a tutorial on how to use it for making microfluidic circuits?
to help you learn it.
Are you wanting to create a parametric drawing such that when scaled, the widths of
curved paths stay constant cross-section? Bend radii stay absolute?
What do you want when scaling?
John
scoc...@gmail.com
Jan 5, 2015, 3:29:20 PM1/5/15
to diy...@googlegroups.com
That's a good question. Let me breakdown the situation for you:
I'm using a brother laser printer (toner) to print a 2D circuit design onto shrinkable polystyrene sheets (shrinkydinks). The shrink rate is about 63%. I'm still not sure what size channels I need so id like to learn a program so I can make the circuits with the least headache. Being able to scale everything would be super since I can test macro-chips and then scale down. Does parameterization involve scripting and hard coding relationships between shapes or is ita trivial task? Thanks again for the offer. I'll try out freeCAD and bother you for tips when I inevitably get stuck. Can freeCAD handle 2D well? Hatching and whatnot? Also if I export a PDF to scale of a micron-ranged drawing, what's the smallest figure that can be drawn? I know PDF is vectorized but when I export in draftsight it thickens and blurs the lines at such small size. Pardon the noobery, I don't dabble much in CAD of any kind until recent. Thanks again!
I'm using a brother laser printer (toner) to print a 2D circuit design onto shrinkable polystyrene sheets (shrinkydinks). The shrink rate is about 63%. I'm still not sure what size channels I need so id like to learn a program so I can make the circuits with the least headache. Being able to scale everything would be super since I can test macro-chips and then scale down. Does parameterization involve scripting and hard coding relationships between shapes or is ita trivial task? Thanks again for the offer. I'll try out freeCAD and bother you for tips when I inevitably get stuck. Can freeCAD handle 2D well? Hatching and whatnot? Also if I export a PDF to scale of a micron-ranged drawing, what's the smallest figure that can be drawn? I know PDF is vectorized but when I export in draftsight it thickens and blurs the lines at such small size. Pardon the noobery, I don't dabble much in CAD of any kind until recent. Thanks again!
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D
Subject: Re: Microfluidics Chat Thread WAS: [DIYbio] Paper request
--
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Learn more at www.diybio.org
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To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/54AAF1ED.7090604%40industromatic.com.
John Griessen
Jan 5, 2015, 4:40:26 PM1/5/15
to diy...@googlegroups.com
On 01/05/2015 02:28 PM, scoc...@gmail.com wrote:
> That's a good question. Let me breakdown the situation for you:
> That's a good question. Let me breakdown the situation for you:
Being able to scale everything would be super since I can test macro-chips and then scale down. Does
> parameterization involve scripting and hard coding relationships between shapes or is it a trivial task?
I think both are possible -- python code or click on to associate.
> parameterization involve scripting and hard coding relationships between shapes or is it a trivial task?
Thanks again for the
> offer. I'll try out freeCAD and bother you for tips when I inevitably get stuck. Can freeCAD handle 2D well?
Sure.
> offer. I'll try out freeCAD and bother you for tips when I inevitably get stuck. Can freeCAD handle 2D well?
Hatching and whatnot?
Yes.
> Also if I export a PDF to scale of a micron-ranged drawing, what's the smallest figure that can be drawn?
Will need to try out.
Let's take this off list next unless others are interested
John Griessen
Jan 5, 2015, 4:57:17 PM1/5/15
to diy...@googlegroups.com
On 01/05/2015 02:28 PM, scoc...@gmail.com wrote:> I'm still not sure what size channels I need so id like to learn a program so I
can make the circuits with the least headache. Being able to scale everything would be super ...
If you simply need direct scaling, and want to make paths with circular arcs connecting them,
usually rectilinear, but sometimes along odd angles, but still with smooth arcs to make bends,
then my favorite electronic printed circuit layout program "PCB" does that well.
John
can make the circuits with the least headache. Being able to scale everything would be super ...
If you simply need direct scaling, and want to make paths with circular arcs connecting them,
usually rectilinear, but sometimes along odd angles, but still with smooth arcs to make bends,
then my favorite electronic printed circuit layout program "PCB" does that well.
John
Nathan McCorkle
Jan 5, 2015, 5:12:49 PM1/5/15
to diybio
On Mon, Jan 5, 2015 at 1:42 PM, John Griessen <jo...@industromatic.com> wrote:
> On 01/05/2015 02:28 PM, scoc...@gmail.com wrote:
>>
>> That's a good question. Let me breakdown the situation for you:
>
> Being able to scale everything would be super since I can test macro-chips
> and then scale down. Does
>>
>> parameterization involve scripting and hard coding relationships between
>> shapes or is it a trivial task?
Parameterization should mean that a given component is parametric,
> On 01/05/2015 02:28 PM, scoc...@gmail.com wrote:
>>
>> That's a good question. Let me breakdown the situation for you:
>
> Being able to scale everything would be super since I can test macro-chips
> and then scale down. Does
>>
>> parameterization involve scripting and hard coding relationships between
>> shapes or is it a trivial task?
connecting components together for a given design is a different phase
of designing things. What I mean is, you would have parametric
channels, but also parametric curved channels, and then you would
connect a straight segment with a curve to create a channel that had a
curved section on the final device.
>
> I think both are possible -- python code or click on to associate.
> Thanks again for the
>>
>> offer. I'll try out freeCAD and bother you for tips when I inevitably get
>> stuck. Can freeCAD handle 2D well?
>
> Sure.
> Hatching and whatnot?
> Yes.
>>
>> Also if I export a PDF to scale of a micron-ranged drawing, what's the
>> smallest figure that can be drawn?
resolution (DPI) a PDF can handle, and then also what max DPI your
output device can handle. The CAD resolution is really just setting
the DPI, what DPI is needed depends on the manufacturing requirements
and the manufacturing system (i.e. laser printer, CNC, SEM/FIB
lithography mask/direct-etch, diffraction-limited lithography). All
these systems have some slop or 'play', it would be pointless to
export with 1 dot per nanometer, if your manufacturing system could
only address 1 dot per 10000 nanometers, coupled with blurring that
might happen too after PDMS replication for example.
>
>
> Will need to try out.
>
> Let's take this off list next unless others are interested
CAD-kernel it is based on is:
large, old, complex, lacking tests
all leading to instability and immense difficulty to maintain/fix/augment.
I started playing with BRL-CAD last night and it looks like it might
be really good. Originally developed by the U.S. military (or at least
their dollars), and has been industry-proven in that sense. The
interface is a bit clunky, but I think it is really bad simply because
no one has made a 'BRL-CAD for dummies' web page somewhere. Once I
figured out what I needed to do, it was quite simply to get a 3D shape
displayed, though I didn't look at exporting it in any formats.
Nathan McCorkle
Jan 5, 2015, 5:14:51 PM1/5/15
to diybio
On Mon, Jan 5, 2015 at 12:28 PM, <scoc...@gmail.com> wrote:
> That's a good question. Let me breakdown the situation for you:
>
> I'm using a brother laser printer (toner) to print a 2D circuit design onto
> shrinkable polystyrene sheets (shrinkydinks). The shrink rate is about 63%.
> I'm still not sure what size channels I need so id like to learn a program
> so I can make the circuits with the least headache. Being able to scale
> everything would be super since I can test macro-chips and then scale down.
> Does parameterization involve scripting and hard coding relationships
> between shapes or is ita trivial task? Thanks again for the offer. I'll try
> out freeCAD and bother you for tips when I inevitably get stuck. Can freeCAD
> handle 2D well? Hatching and whatnot?
If you're talking about this:
> That's a good question. Let me breakdown the situation for you:
>
> I'm using a brother laser printer (toner) to print a 2D circuit design onto
> shrinkable polystyrene sheets (shrinkydinks). The shrink rate is about 63%.
> I'm still not sure what size channels I need so id like to learn a program
> so I can make the circuits with the least headache. Being able to scale
> everything would be super since I can test macro-chips and then scale down.
> Does parameterization involve scripting and hard coding relationships
> between shapes or is ita trivial task? Thanks again for the offer. I'll try
> out freeCAD and bother you for tips when I inevitably get stuck. Can freeCAD
> handle 2D well? Hatching and whatnot?
https://en.wikipedia.org/wiki/Hatching
I don't see why you would want that. It seems for your case, you would
want greyscaling, which would be a feature of your 3D slicing
operation most likely.
--
-Nathan
Tom Hodder
Jan 5, 2015, 8:03:22 PM1/5/15
to diy...@googlegroups.com
On Monday, 5 January 2015 20:17:25 UTC, John Griessen wrote:
On 01/04/2015 06:23 PM, scoc...@gmail.com wrote:
> Anyone have a favorite tool and is willing to post a tutorial on how to use it for making microfluidic circuits?
Not exactly, but FreeCAD is likely up to it. Would be happy to do a test draw in parallel with you
to help you learn it.
+1 for freecad
(particularly after putting the effort into to get over the initial learning curve... which if you haven't done solildworks is significant)
Though I am at the stage where I would like to assemble complex items from freecad parts, and its lacking those features atm. Any suggestions on how to proceed there?
John Griessen
Jan 5, 2015, 10:17:39 PM1/5/15
to diy...@googlegroups.com
On 01/05/2015 07:03 PM, Tom Hodder wrote:
> I would like to assemble complex items from freecad parts, and its lacking those features atm. Any suggestions on how to proceed
> there?
I would sign on to their forums and ask Yorick about that. He's done plenty of combining together
> I would like to assemble complex items from freecad parts, and its lacking those features atm. Any suggestions on how to proceed
> there?
of parts to quickly make models in Blender for architecture purposes, so he'd
know about the state of FreeCAD, and tricks to get it
to work.
Nathan McCorkle
Jan 5, 2015, 10:39:45 PM1/5/15
to diybio
On Mon, Jan 5, 2015 at 7:20 PM, John Griessen <jo...@industromatic.com> wrote:
> On 01/05/2015 07:03 PM, Tom Hodder wrote:
>>
>> I would like to assemble complex items from freecad parts, and its lacking
>> those features atm. Any suggestions on how to proceed
>> there?
>
>
> I would sign on to their forums
The freenode.net IRC room has been quite responsive when I've asked
> On 01/05/2015 07:03 PM, Tom Hodder wrote:
>>
>> I would like to assemble complex items from freecad parts, and its lacking
>> those features atm. Any suggestions on how to proceed
>> there?
>
>
> I would sign on to their forums
questions there
Tom Hodder
Jan 6, 2015, 2:05:16 AM1/6/15
to diy...@googlegroups.com
lol I'm in there already. I see you posting... ;-D
Jonathan Cline
Jan 28, 2015, 4:09:33 AM1/28/15
to diy...@googlegroups.com, jcline
On Sunday, January 4, 2015 at 4:23:51 PM UTC-8, Sebastian wrote:
So I really can't find an easy way to make circuit designs. I tried libreCAD, DraftSight, and inkscape and it seems that scale and simple shapes is really annoying to do. I'm about to either draw it by hand with epoxy and a needle tip dispenser or use MS Paint.
If you are using Macintosh, try OmniGraffle (the closest, but much worse, Microsoft windows equivalent would be Visio; unfortunately, Microsoft has ruined a lot of Visio functionality since it's acquisition into MS Office years ago). Both of these are sophisticated non-CAD drafting programs. Omnigraffle will do SVG. If you are not on a Mac, ask yourself, "why am I hurting myself?". Many of the published 'proto-circuits' from Lab on a Chip journal at least from 2007-2010 date range were drawn in MS Powerpoint (which I never recommend using for any purpose at all). If you plan on printing shapes with a laser printer, be aware of the printer's scaling.
Forget CAD programs, you're not trying to become a mechanical engineer, you just want some precisely dimensioned circles and rectangles and angled lines.
## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################
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