Mibo for smartphone microscopy

With a simple addition of a lens in the front, and a homemade stage, a smartphone camera can be converted to a microscope.  AVI Labs from Turkey ran a Kickstarter campaign to mass produce a set of lens (and support) for converting a phone camera to a microscope, and my “mibo” kit arrived today.  The child in me spent entirely too long playing with it.

mibo as arrived
mibo as arrived: a bundle of plexiglass, and an instruction sheet.

There is not much to say about the kit.  It comes as a few sheets of cut plexiglass, some lens, and an instruction sheet.  A few items are missing from the kickstarter package: no “velvet bag to prevent scratches”, and no light source.  I am supposed to receive two sets, but one of the sets misses the back plate.  Everything feels a little flimsy.  There is an iOS app, but I have an android phone so I can’t comment on that.

Mibo assembled.
Mibo assembled.

Assembling the kit takes ten seconds, involving only snapping together five sheets of plexiglass.  The circle on the top plate is where the lens gets inserted.  The sample stage has magnets glued on either side, and the thinking is that it can be minutely controlled using the magnets on the outside.  The stage didn’t work very well, and I certainly would have preferred a nut / carriage bolt adjustment mechanism.  Most of the time the adjustments are made with eyes on the screen, and I find it difficult to keep the stage horizontal.  The sample slide can then slide down, and all the adjustments for null.

My sample stage also seems a hair too wide for the box, and it sticks occasionally, making fine adjustments difficult.  And then… one of the magnets just fell off.  The way the sample is mounted didn’t work for me, and I may just rig my own sample mount later.

Once the stage is correctly set, however, the lens does its job perfectly.  I could not make sufficiently fine adjustments to the stage, so I’ve (for now) given up on the mibo+ kit (80x base magnification).  The following pictures are taken with a Sony Xperia Z2, lighted ~30 cm from the stage using 300W lights in a softbox, and with just a single lens (40x magnification, zoom to 160x).  The original pictures are 20 megapixels in size.

A name card showing the 40x magnification (no zoom)
A name card showing the 40x magnification (no zoom)

Here are a selection of items we will be looking at closely.  It’s fascinating what they look like up close.

Items looked at using the microscope.
Items looked at using the microscope.

Click on an image to view a higher resolution version (careful – large file size!)

Our “Course Outline” Display

I teach chemistry, but I am a kindergarten teacher by heart.  I favor the bright, vibrant, tactile, and physical.  I’m also deeply of the meta persuasion, believing that one must care about the details but never lose sight of the bigger picture.

As the school year kicks off, I mused about how to present the course outline.  Do I send off two pages of PDF?  Do I send off a spreadsheet?  Should it be “moodle-lized”?  The progress should be planned, and the plan clearly communicated to students and co-teachers.  But the plan must also be flexible.  The best of planners draft plans that survives unscathed with reality; I am not one of them.  (There are also plan-pushers-come-hell-or-high-water, but I’m not one of those either.)

There happened to be an empty board outside the lab/classroom, and I decided we’ll do a bright, vibrant, tactile, and physical display!

How should it be structured?  The structure of the display has to conform with the inherent structure of the calendar.  At UWC Hong Kong, academics are structured in cycles, with 7 different academic days in each cycle.  Each day contains 5 classes.

The 7 different academic days — note that A always precedes B, B before C, and so on.

The upshot is that each class is present for 5 times in a cycle.

All classes happen 5 times in each cycle.

Which means that instead of labeling lessons sequentially with 1, 2, […] 40 for a term, they can be organized instead into cycle 1 – class 1 (1-1), cycle 1 – class 2 (1-2), […], 2-1, 2-2, […], 8-5.  Which means a single term with 8 cycles can be planned with a grid like this:

Or, in my world of card-board and stickies, this:

Planning an academic term
Term planning with color stickies and big sheet of paper

Now it’s time to work on the actual board!  Outside our lab there’s a pair of big white-boards, so I went with measuring tape and markers, to doodle and erase and doodle and erase while contributing to the mosquitoes’ welfare.

Scribbling on the white-board with markers. The basic idea here is conserved to the end, but the final display was corralled into the board on the right.

Some drawing, fidgeting with sizes, printing, shopping, cutting, laminating, more cutting, more shopping, and a thousand little unexpected minutiae later (quoting Sally Brown, “Fold? Crease? Cut?! WHY IS IT SO COMPLICATED?!“)… we have our bright, vibrant, tactile, and physical display!

The “course outline” display by mid-term time.

 

Hong Kong is humid and sometimes windy, which means that anything affixed by tape falls off shortly.  Tape also makes it (relatively) hard to move elements around.  A solution to this dual problem is to use neodynium disc magnets (1mm thick, 10mm diam.) to attach all pieces to the board — they are at once strong enough to keep things on, and allow simple repositioning.

A cycle is represented by a laminated strip with 5 boxes, each perfectly sized for a 3″ post-it note.  I got 5 colors of sticky-notes, each signaling a different kind of event:

  • yellow: a HL/SL class
  • orange: a HL only topic
  • green: lab
  • pink: test!
  • blue: homework.  This sits on a parallel track, and comes with arrows to show when they are expected.

Each sticky-note describes the subject for the day, the relevant topic in the IB syllabus (e.g., “periodic table” is 3.1), and page number references for different textbooks.  I try to update it about a week ahead, so students can read ahead for class if they care enough.  (Some EAL students appreciate being able to do this.)  It seems fine enough for what we need (survey to students at end of term), but this was not the original idea.

The original, more ambitious idea was to hold all the additional information (syllabus, text page#) in a companion website which has systematic URLs.  (For example, topic x.y is always represented as www.jkwchui.com/IBchem/xy)  Then we can paste onto the post-its stickers with only topic numbers and QR-codes: all that the students need to do is either to search the topic number in the website, or scan the QR-code.  This will be tied in to the Badges system too (a “Steam achievements”-like awards for above-and-beyond efforts):

What happened?  To my chagrin, I greatly overestimated my abilities.  I thought I can teach new curricula (chem+ToK), lead new activities, supervise 5 EEs, and simultaneously be writing and illustrating “the best interactive IB chemistry” website.  It’s so crazy I don’t even know why I tried…

(But then, it’s so crazy it might just work!)

Clocks of History (Chinese Dynasty edition)

This was something I worked on-and-off in Spring/Summer 2012.  I won’t have time to finish this until much later.  It sitting on my drive does no one good.  If you’re interested in the project, I’ll be happy to get in touch with you to set the idea free.

History is usually represented as a sequential time-line, stretching from the beginning on the left to the end on the right.  As a picture-thinker I have a hard time visualizing and placing in events.  Our visual width is usually not enough to take in the entire span, and if it is zoomed in, I quickly lost sense of the scale and reference to events outside the current view.

When I see a zoomed in view, I get the relationship between the events within the “scene”. I can tell that M precedes N and P. However, unless the history is already intimately familiar to me, I have only a faint idea of where and how far A and G are relative to the field of view.

I would be surprised that Richard the Lionheart is as far away from Shakespeare as Shakespeare is from us, or that Cleopatra is temporally closer to the moon landing than the construction of the pyramids (h/t wonderfuldog on Reddit).

This becomes even more of a problem when different sources or systems of time is used.  In particular, I had absolutely no sense of whether the Tang (唐) dynasty co-exists with Jesus, St Augustine, or Thomas Moore.  (The answer is “none of the above”.)  I really wanted to make sense of this once and for all.

The solution, I thought, was to roll time into a clock, so that each point in time sits at a unique spatial location.  (I first came across a mentioning of this in a lecture by a Catholic priest around 2004, whose name I have long forgotten.)  The challenge was then two-fold:

  1. establishing a useful scale, and
  2. preparing it allaccurately.
I did say bones, didn’t I?

Since history had no beginning or end, the choice of a scale (and thus ends) is necessarily arbitrary.  I sketched out all reasonable combinations: scale of 100-500 yr / “hour” against sliding the end-times from 2000 to 2200.  For the history I’m interested in (where meaningful oral / written records exists), a scale of 300 yr/hr ending at 2100AD worked best.

The outstanding problem is to chart things accurately (and not break too much sweat about it).  I wrote some simple Processing code that sketches out a backbone of the a tab-delimited text file of (i) spot events, and (ii) events with duration.

(The code is nothing to write home about.  It simply converts time into polar coordinates, and draw arcs on the frame.  It really should do more to help the next steps, but that’s what I don’t have time for!)

I could then bring the backbone into Illustrator to spice it up, and overlay different timelines together.  The final output for Chinese dynasties against European civilizations is shown here.  (With the usual disclaimer that periods are fuzzy around the beginning or end; dynasties and periods often languish and blend into the next.)

[gview file=”http://www.jon.hk/WP/wp-content/uploads/2012/11/ChineseDynasties.pdf”]

The final output surprised me on a few things:

  • The brevity of the Qin (秦) dynasty — after uniting a China which had been at war for 600 years (!), this dynasty only lasted for a paltry 19 years.
  • The chaos that was historical Europe.  It turned out to be extraordinarily difficult to sketch out detail timelines for Europe, since borders, names, faith, factions, and races are all continuously shifting and war was perpetual.  It seems to be more fruitful to speak of defining (localized) events rather than (large scale) patterns, but I’m no historian.  (On that note: pundits jeer at the selection of the European Union as a Nobel Peace prize recipient, but one would be hard-pressed to find a (Western) Europe in peace for 60+ years.  Taking the long view, the period of peace we dwell in is truly remarkable.)
  • The even longevity of Chinese empires.  The “registered” dynasties all have lengths within the same magnitude, and there does not seem to be a hastening of pace as time marches on.  I’m mystified onwhy should lifetimes NOT be power law distributed, given that mass riots are power law distributed (note to self: citation needed).

The future of the project: what I’d like is to move the entire work-flow into Processing, and use Processing.js to make this an interactive application that readers can zoom-in/out, filter, and get access to more details via tool-tips.  A poor man’s Simile Timeline, but with a meaningful beginning and end.  If you want to help out, or take the idea and run with it, give me a shout and I can get the (ugly, elementary) Processing code to you.

Painting: Lonely Winter Tower

Painted from several photo references in Photoshop CS5, took about 90 min end-to-end.  It’s been awhile since I’ve pushed pixels, and the entire process feels quite foreign and unbearably long.  I got pretty impatient with the details that needed to be filled in half way through, so it ended pretty rough and sketchy.  And then, it was not until the end that I realized that, somewhere along the way, I’ve reflected the tower and #$^&% up the light source :(

Edit 8 Jan: This was in part exploring a way of generating generic, modular art, particularly useful for creating cut-scenes in open-source games.  There’s quite a few things that need to be solved, particularly as it relates to perspective, color harmony, usability, and sheer time required to bang out large number of them.  In a way this is like creating high quality, irregular, non-isometric sprites.  One of the explorative attempt was using vector as the source (seeing that it’s my preference), keeping a simpler style.  I didn’t like the output, however, and the search continues.

Wikipedia Illustration: 2011 Highlights

Happy new year!  As clock strikes midnight and 2011 came to a close, I was working on a illustration for Wikipedia.  In two generations, I think the open-source and collaborative movements will be two of the highlights on the gravestone of our time; never before in history have people been able to come together to construct intellectual monuments with neither carrots nor sticks.

Looking back at 2011, I was surprised to find that I’ve uploaded >100 illustrations for WikiCommons (even with a thesis to write/defend, and 3 months hiatus in the Andes & Rockies).  Most of these are simple vectorization requests from the Illustration Workshop that’s nothing to write home about, but a few integrates a breadth of information into interesting figures that I ended up being proud of.  Here’s that gallery.

Chloralkali process illustrates how NaOH and chlorine gas is made by electrolysis.  This figure made extensive use of Illustrator’s symbols feature to generate the population of molecules, and the shape-builder in CS5 for simple construction of the irregular container and “solution” from elementary shapes.

Berimbau parts seeks to prepare a vector image with labelled parts.  The benefit of having information in a vector form (particularly, as a SVG) is that the file itself is a plain-text document that can be easily modified with Notepad, making translation possible with little efforts.  For this particular image, the technical challenge was in converting Illustrator’s gradient meshes to something that can be used by Wikipedia’s SVG engine.  The final process involved converting it to a raster image, Live Trace, and manual tweaking.

SSME schematic shows how fuel and oxidizer gets mixed to provide thrust for a space shuttle.  The illustration was mostly constructed with the pen tool, together with the shape-builder.  The outline layer was lifted and duplicated, with the underlayer converted to a live paint group and painted.  The time consuming part was understanding what is actually going on, given the sources were quite confusing and out of my area of expertise.

Thalamus structure illustrates the different parts of the thalamus… which is once again not in my area of expertise and required outside reading.  (Not that I remember very much about it.)  I’m very fond of expansion to show context and multiple scales.  The human image was a high-resolution raster, with pen tool tracing of outlines.

US Air seating chart – This one I’ve written about before.

Sogen Kato home floor-plan describes the discovery of the mummified body of a “100+ yr old” Japanese man, whose family hides the fact that he was dead in order to keep collecting government cheques for over 30 years.  The image was made with Google Sketchup – my first exposure to the tool.  I’d go on to learn about Sketchup in much more detail later in the year.

Wheat nutrition combines information from multiple sources into one coherent image.  The image is not as nice looking as it was executed – wikipedia’s SVG engine does not support either gradient mesh, symbols (as is), or pattern fills.  It also display SVG fonts inconsistently in thumb-nails and final rendering, and between assigning fonts from Inkscape or Illustrator – that’s one that I still haven’t figured out completely.

Overview of Spectrscopy sought to combine the elements involved in spectroscopy in one image, so that the main text can have visuals to refer to.  There’s a few implicit elements in there coming from teaching spectroscopy for a few years – I think experts would get appreciation of this that novices wouldn’t.  The shapes were constructed with the 3D functions in Illustrator, and this prompted the thought of creating the ongoing OpenChemArt project.  This diagram had been translated into several languages.

Reedbed treatment ponds describes different methods for water treatment.  This is one of the first “ambitious” images I tried to make for wikipedia, combining multiple sources of information and representing them in a coherent way.  The single-point perspective was drawn in as is – in CS5 (which I didn’t upgrade to until August) there’s a new perspective tool which might have been useful.

In 2012 I’d like to explore “messier”, painterly vectors.  It’d require some formal trial-and-error to see where the limitations of SVG in Wikipedia arises.  I’d probably also get myself into the raster realm again, since that’s likely where I’ll be when working with the iOS apps I’d like to write on the side.

Pictorial Guide to Thin Layer Chromatography, feat. Lego

In the several years that I tutored at the 1st-year help center, I’ve always had students who find thin-layer chromatography mystifying.  Most of these students don’t “get” what the plates are doing, or the role of the eluent.  For whatever reason, the physical analogy of things getting washed away and gripping the ground (or the inability to do so) seems to help in guiding the thought process.  I drew this up should you, as either instructor or student, would find this helpful.  Lo!  Behold the whimsical…

As usual, clicking on the figure opens a larger version for viewing.  A PDF version for print is available here. I’m not too happy with the final output – I feel as if the spatially-suggested connection between the analogy and the phenomena to be explained is not clear enough.  Suggestions to make this more useful / analogy more clear is appreciated.

Update (17 Dec 2011 Revision R3): The addition of the imagine/now consider label seems to clear up the analogy-phenomena.  I thank Loïc Samuel for the suggestion.

Interpreting Proton NMR – Overview

A bird’s eye view of 1H NMR spectra interpretation in comic form.  Here we first dissect the visual mess into the three major components implicit in every peak, and then systematically approach each component to show the connection between spectral information and molecular parameters.  Click on the image to expand; for printing, a resolution-independent PDF is available here.

Side-note: a number of people have been looking for this to be published in the last year.  If you’re one of them… I’m sorry for the tardiness!  NMR is the flagship of organic structure identification, revealing much more information than techniques like IR; the corollary is that interpreting NMR is a bigger and more nuanced topic than comparable techniques (on both interpretation and theoretical grounds).  I’ve been going back-and-forth the drawing board to select the right amount of content to include in this overview, and what to reserve for others.  Hopefully this final version is a good compromise.  I encourage and appreciate your comments and questions, and will make updates to the spread with your feedback.

Side-note 2:  Do you speak another language and would like to see this translated?  Contact me and we’ll try to work something out.

Update (R4, 15 Dec 2011):  Updated with corrections.  I thank Shaun MacLean (U of Manitoba) and James Ashenhurst (Mastering Organic Chemistry) for their helpful suggestions.

Sketchy Friday – Capoeira

A sketch of a capoeira player doing an role (a rolling escape along the ground).  ~15m, Adobe Illustrator, mostly with the brush tool with basic brush, except for the trails which were drawn with a (CS5) bristle fan brush.

I had a hard time visualizing the contorted limbs and perspective in my head — the beginning gestures are very profile-like (and stiff).  I’m particularly not happy with the right calf, core, and last minute head change, but I do like the dynamics in the final version.  In December I really need to get myself strapped down to finish Riven Phoenix’s Structure of Man series of tutorials before I start on my magnum opus.

Lovebirds (illustration)

While working on a piece of explanation about thin layer chromatography, I got side-tracked into making this illustration (and this detour actually makes perfect sense when it all comes together).  The picture’s all vector, and if you pick up the PDF version it can be printed to high resolution and remain crisp and clean.  The source of the penguins was a plush-toy that you can find here.

Pretty Picture of Messy Membranes

I’ve been reading the biophysics literature on lipids in preparation for the defense, particularly in connection to phase transitions, transient pores, and lipid ion channels.  If you’re at all interested in membrane transport, you’ll find Heimburg 2010 and Salgado 2011 fascinating.

I’ve long known that lipid membranes are messy, but I had not came across a clean distribution profile of the messiness until today.  The original, however, was in 7 shades of gray that even my eyes can’t tell what was going on.  After sketching out for myself what it would look like (and some iterations of cleaning up) we ended with a pretty sweet poster of lipid EDP:

If you’re looking to print this out, you should do that from the PDF print linked below.

[one_third][learn_more caption=”PDF”] Download[/learn_more][/one_third]