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Monday, December 26, 2011

Fwd: Re: Questions about the microscope needs of the community

---------- Forwarded message ----------
From: "Simon Quellen Field" <sfield@scitoys.com>
Date: Dec 26, 2011 11:01 AM
Subject: Re: Questions about the microscope needs of the community
To: <diybio@googlegroups.com>

I demonstrated a $30 DIY microscope at Science Hack Day that was getting
sub-micron resolution. The images came out quite a bit better than the
webcam or cellphone microscopes, because the design replaced the lens
of a digital single lens reflex camera with a microscope objective, so the
only thing between the 18 megapixel sensor and the subject was a good
quality microscope objective ($25, plus about $5 in plumbing parts).

When I am done writing my latest chemistry book (mid January) I will
resume work on an XYZ stage for it.

The idea is to mount the stage directly onto the objective lens barrel, so
that vibration is not an issue (that's why standard microscopes are big heavy
steel beasts). With an automated XYZ stage, I can have the computer take
the thousands of images needed to do the gigapixel imagery I currently do
way through thick samples like ants and fleas. Hundreds of these stacks are
then stitched together using panorama software to get huge images of the
entire area under the cover slip.

I expect the result to be a DIY microscope for well under $100 that can do
automated imaging in three dimensions at resolutions under 500 nanometers,
using oil immersion objectives.

By using panorama stitching, you can get the same results with a $50 objective
that you get with $3,000 objectives, since you use only the center of the
field, where the cheap objectives are as sharp as the expensive ones. You use
a longer microscope tube so that the sensor is filled with only the sharp
center of the objective's field of view. Then you move the slide around, taking
lots of shots, and merge them together in the panorama.

With regard to describing the quality of the image, forget about magnification
(such as 100x, 500x, etc.). What matters is resolution. Us a stage micrometer
to add scales to your images, so that the sizes are apparent to anyone viewing
the image. On a computer screen or a cell phone screen, magnification is going
to change with the size of the screen. But resolution will not, and resolution is
what you are after anyway.


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On Mon, Dec 26, 2011 at 5:52 AM, Marc Dusseiller <dusjagr@gmail.com> wrote:
hei folks,

as you might have seen, on the hackteria site there is looaads of tips
to for the DIY microscopes. as i have done many workshop on the topic,
built around 300 with participantss...
http://hackteria.org/?cat=15

we, gaudi, mac and me, already developed a few ideas using laser cut
designs:
http://hackteria.org/wiki/index.php/Laser-cut_microscopy_stages

the key thing is always a lever system to gear down the motion of the
stage from the screw. a classic mechanical model... for a few thousand
years :-)

talking about magnification, please refer to numbers like "field of
view" and compare it to the digital resolution of the image. i always
wanted to get my hands on some fluorescent calibration beads to get
the "point spread function" using the hacked PS3 eye cam, with
inverted lens and other cheap lenses. havent done it sofar. but i did
some experiments on fluorescence detection in general, also with the
PS3 eye (a must in this case, due to its sensitivity, and there seems
to be hacks to prolong the shutter times). key is to remove all other
light sources, loads of black stuff around the cam etc... the stuff i
used was highly labels microbeads, so i dont know about detecting
transfected cells.

also, got great results from checking human blood cells, single cell
yeast etc.

i'll be working on an improved documentation the next few weeks during
my residency in indonesia, stay tuned.

all the best



On Dec 26, 9:19 pm, Jonathan Nesser <jonathan.nes...@gmail.com> wrote:
> I don't take it as "hating" at all, I'm pretty isolated where I live,
> so I don't have a lot of chancefor discourse about my ideas, this is a
> welcome chance to question my own thoughts and conclusions. My price
> point is surely less than $500 dollars, more likely less than $250,
> and I suppose my angle in all of this is that there does exist
> decently priced microscopes that are quite powerful... My problem with
> the existing market is I've only found one Inverted microscope for
> less than a thousand dollars, it was a pocket model with an unmoving
> stage, no digital capture, and didn't even look to have the clearance
> to accept a standard tissue flask (I can't recall the name of the
> manufacturer right now, but it was billed as a pocket inverted
> microscope). This is a problem to me, as it doesn't seem like the
> parts/knowledge to build an inverted digital capture only microscope
> require that price point. The reason for this obsession with inverted
> models in general is that it is yhe only way to observe active cells.
> This has applications ranging from the use of fluorescent protein and
> dye probes to obtain data about the workings of cells, to studying
> cancer cells (morphology of tumors, measuring growth rates of cells,
> etc) and to artists creating work based on live cells. While I'm not
> sure bacteriology will be the killer app for this microscope system
> (and it is designed to be a system, interchangable, modular, made to
> do what you want it to do, not what i the designer can forsee you
> wanting to do), I do think this will be a godsend for anyone working
> with eukaryotic cells or tissues. I look forward to responding to
> anyone else's questions or concerns, please do remember to put down
> what your desired stage sizes would be as well though :)
>
> Jonathan Nesser
> jonathan.nes...@gmail.com
> diybioandneurosci.blogspot.com
> Written on a tablet, excuse the lack of formatting and any other
> errors.
>
> On Dec 26, 5:19 am, Avery louie <inactiv...@gmail.com> wrote:
>
> > @ Dakota: Long time no see, man.  What are you imaging these days?  I have
> > found that sticking the business end of a point-and-shoot digital camera
> > directly onto the eyepeice of the scope and using macro mode works pretty
> > well.  I took a nice picture of some algae, as you can see
> > here<http://tequals0.wordpress.com/2011/12/18/diy-bio-postcards-biolumines...>.
> > That is actually what it looked like- the microscope was all out of
> > alignment and not all quite there, and thats what it looked like to my
> > eyes.  Its still a pain, but it's not bad if you want a few pictures.
> > Also, immersion oil is surprisingly cheap- like 6-10 bucks!  I might pick
> > some up for my next project, so let me know if you need some.
>
> > What is your price point or "angle" for this scope?  It seems like a fine
> > project, but american science and surplus sells a monocular 40x 100x and
> > 400x scope that is 12" tall, for ~60 bucks, and what seems to be the "nice"
> > version for ~102.  There is also a 150x (max) USB scope for ~60 bucks.  I
> > have seen amazing things from the eye, and I hope to see amazing things
> > from this project, but it might be worth more to the community to have a
> > nice stage that they can stick commercial "usb microscopes" into.
>
> > I am not trying to hate on your project, just curious.  Are the sketches
> > posted anywhere?
>
> > --A
>
> > On Sun, Dec 25, 2011 at 11:35 PM, Jonathan Nesser <jonathan.nes...@gmail.com
>
> > > wrote:
> > > I'm looking at something in the realm of 120X total magnification
> > > (just an estimate compared to a crappy high school grade microscope,
> > > nothing to benchmark against) with quite clear image quality (no
> > > obvious chromatic or spatial distortions, good focus) with the system
> > > I'm using now, though I've tried to design it with portability
> > > (multiple magnification settings, easy hacking of attachments) in
> > > mind. Currently I'm just extending the distance the lens system is
> > > from the light sensor by means of a metal tube, which you could switch
> > > out fairly easily. This works with the leap from 50x to ~120x
> > > magnification, but because of the corresponding decrease in working
> > > distance it may not work for the leap from 100x to 400x. The final
> > > production system may have to rely on a commercial LWD objective to
> > > get high magnifications like that, but I'd like to stay away from that
> > > if at all possible (cost and mounting issues, though I wouldn't be
> > > opposed to having an add-on kit for mounting such a thing). The metal
> > > tube system may work if I can find a lens with a longer base working
> > > distance, but I'm limited in my ability to go out and buy a bunch of
> > > webcams to test them all. Currently I'm using a logitech C270. I think
> > > the PS3 eye guys have been getting something closer to 400x, though I
> > > don't know about their working distance. Also, adapting the ps3 eye
> > > means using glue on the optics to reverse it (which means
> > > interoperability is out, unless I can figure out a way to make new
> > > lens mounting hoods for these with a 3d printer, the dimensions are
> > > finicky and would make such a print pricy though).
>
> > > As far as what I'm making it for, personally I plan on using it as a
> > > general field microscope (general bio observations, just for fun type
> > > stuff), and significantly for making observations of fluorescence
> > > altered neuron cultures. I'm less worried about my specific
> > > applications than the communities demands though, because I would like
> > > to eventually produce kits for others in the diybio community to use
> > > as well (possibly creating a revenue stream to fund my own research),
> > > which is why I ask what others would likely use something like this
> > > for. As far as possible uses go, the microscope is designed to have as
> > > much open space around the stage working area as possible to allow for
> > > attachments (manipulators, sensors), and the light system is designed
> > > to be able to accommodate light filters, darkfield, etc.
>
> > > Basic design idea:
> > > The microscope frame is a square or rectangle, hollow at the level of
> > > the stage, the stage is a thin clear piece of glass with a frame,
> > > suspended in the center of the microscope frame with rods. To
> > > manipulate a container you just place it on the stage platform, the
> > > container doesn't move on the stage, the whole stage moves. Think of
> > > the stage as a 3d printer build platform in two dimensions, x and y.
> > > Movement of the stage platform is designed to accommodate viewing of
> > > anything that can fit on the stage platform itself. As far as plans
> > > for magnification, I'm trying to get the largest range of
> > > magnification possible while still maintaining a working distance
> > > usable in an inverted microscope setup, which may preclude
> > > magnifications of 400x, but hopefully will be able to at least
> > > accommodate 200x.
>
> > > Jonathan Nesser
> > > jonathan.nes...@gmail.com
> > > diybioandneurosci.blogspot.com
>
> > > On Dec 25, 8:39 pm, Avery louie <inactiv...@gmail.com> wrote:
> > > > I would use the microscope for bacteriology. The standard dishes are
> > > about
> > > > 10cm (100mm) across.  However, it also depends on what you are using your
> > > > microscope for.  Unless you can get a good image at 400x, you aren't
> > > going
> > > > to see individual bacteria, and even at that level they are about the
> > > size
> > > > of a grain of salt.  The SOP in my lab is to just take a sample from the
> > > > dish and prepare a slide, not to look at the plate itself because of
> > > > contamination and practicality issues.  If you ware making something more
> > > > like a dissecting scope, for looking at colony morphology, I would say
> > > that
> > > > you would want to have something that can access any part of the round
> > > > plate--because you never know where the colony will be.  Otherwise, just
> > > > make it slide-sized.
>
> > > > What kind of magnification are you getting?
>
> > > > On Sun, Dec 25, 2011 at 9:25 PM, Jonathan Nesser
> > > > <jonathan.nes...@gmail.com>wrote:
>
> > > > > I've recently been thinking about microscopes. My thought has been to
> > > > > make a kit for a webcam style microscope, inverted of course, because
> > > > > we're concerned with observing actual working cells not dead and
> > > > > mounted ones. The only thing that is really an issue is creating a
> > > > > stage for such a system (optics having already been solved for the
> > > > > most part by the guys working on stuff like the ps3 eye microscope,
> > > > > etc.) I think I've finally cracked the issue of an inverted stage that
> > > > > would be build-able with simple parts, and I'm looking for some input.
> > > > > Assuming we're only talking about working surface area, how much space
> > > > > would you need on a microscope stage? What sizes of culture flasks/
> > > > > petri dishes does everyone use? If you could, post two numbers, an
> > > > > idealized size that would fulfill your wildest dreams (if you're the
> > > > > type who dreams about this stuff, lol, I know I am), and the smallest
> > > > > space you could make due with realistically. Thanks for your
> > > > > participation, I'll try to put up some pictures/scans of design
> > > > > sketches some time soon, I've just started learning google sketch, so
> > > > > no 3d models as of yet, just pen and grid paper drawings.
>
> > > > > Jonathan Nesser
> > > > > jonathan.nes...@gmail.com
> > > > > diybioandneurosci.blogspot.com
>
> > > > > --
> > > > > You received this message because you are subscribed to the Google
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> > > > > "DIYbio" group.
> > > > > To post to this group, send email to diybio@googlegroups.com.
> > > > > To unsubscribe from this group, send email to
> > > > > diybio+unsubscribe@googlegroups.com.
> > > > > For more options, visit this group at
> > > > >http://groups.google.com/group/diybio?hl=en.
>
> > > --
> > > You
>
> ...
>
> read more »

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