Designing 3D printable Lieberkühn Reflectors for macro- and micro-photography

Designing a Lieberkühn Reflectors for macro- and micro-photography

A Lieberkühn Reflector gets its name from one Johann Nathaniel Lieberkühn, who invented the speculum that bears his name which you may recognize from reflective headband decorations for doctor costumes. The name is generally changed from “speculum” to “reflector” when referring to optical reflectors used in photography and microscopy, perhaps because the term has drifted from its original Latin root meaning “mirror” to refer to probing instruments for dilating orifices.

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Lieberkühn reflectors were a way to bathe an opaque specimen in fill light. Lieberkühn reflectors and their use have unfortunately fallen by the wayside with the advent of modern conveniences like LEDs and fiber optic illumination. The above example from the collection of the Royal Microscopical Society displays a Lieberkühn on a simple microscope. In use, the reflector would be pointed towards the specimen, and fed light by a second mirror like the one on the rightmost microscope. Both of the microscopes pictured were on display at the Museum of the History of Science in Oxford

The working part of the Lieberkühn reflector is a parabolic mirror, which doesn’t add the spherical aberrations of hyper- or hypo-bolic configurations. As an added benefit, mirrors don’t tend to add chromatic dispersion or other aberrations associated with refraction (though they can effect polarisation). A parabola can be described as a a particular slice through a cone , but for the purposes of my first prototype, the functional description in cartesian coordinates will do.

y = alpha x^2
Where alpha depends on the focal length of the parabola.
alpha = 1 /4 f

To get a functional, 3-dimensional mirror, I describe the parabola in terms of the focal length and a given radius as a 2D trace and spin it with rotate_extrude() in OpenSCAD. Leaving an aperture in the middle leaves room for light to reach the objective. The reflector shown below has a 4mm central aperture for the objective, 16mm focal length and 32mm diameter.


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I have sent a few prototypes (matched to particular lenses or objectives) to Shapeways for prototyping. After some characterisation these will appear on theBilder shoppe.

The Oxford Museum of the History of Science is full of beautiful brass and glass

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As part of my tour of Europe I visited Oxford in southern England. A personal favorite was the Museum of the History of Science.

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When Albert Einstein came to Oxford to give a seminar in 1931, someone saved the chalkboard and now it is in a museum. Never erase chalkboards after seminar?

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They had an ample collection of vintage microscopes, including these of the single lens variety.

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The Leeuwenhoek microscope replicas are museum pieces in their own right: 1800s recreations of 1600/1700s technology. You can see that the simple objective is stopped down substantially, limited by a small hole in the brass. Simple microscopes had better resolution than their early compound counterparts, which suffered from the aberrations brought on by all the extra optical elements. Single lens microscopes, essentially ball lenses, mainly suffered from spherical aberration, which can be decreased by limiting the aperture diameter as seen above.

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I am fairly certain the objective on the above simple microscope is mounted upside down, but that gives us a good view of the Lieberkühn reflector. The reflector, a concave mirror around the objective lens, was used to illuminate a specimen with epi-fill light across a wide range of angles.

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The Oxford Natural History Museum was down for maintenance, but I walked through on the way to the Pitt Rivers Museum. The Pitt Rivers Museum includes shrunken heads (the trick is to take all the head parts out first) among many, many other specimens. Even a modicum of interest in anthropology will keep you in the museum for hours.

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The Radcliffe Camera may be my favorite building in Oxford. It is much larger than it appears in pictures. Compare the view through a not so wide-angle lens (above) and wide-angle lens (below).

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I tried to capture the schlieren effect created by the heat rising from this juggler’s clubs, which you can make out on the right edge of the tall building in the background.

Open Access Death Knell. Or Is It?

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I told you publication was a fiat currency

Last week, Science published a critical investigation into the state of peer review in open access journals. John Bohannon, the author,  generated a faux paper describing a set of fictional experiments testing the effects of secondary metabolites from lichen on cultured cancer cells. These papers were sent to a selection of open access journals sampled from the Directory of Open Access Journals (DOAJ) and Larry Beall’s infamous list. The lichen species, secondary metabolite, and cancer cell line were varied randomly to generate iterations of the paper with slight differences, but the shoddy results were the same in each. In a few of the iterations I examined, the structures didn’t even match the secondary metabolite described. The researchers didn’t exist, their names random combinations from a database of first and last names with random middle initials, and the institutions they worked at were fictional. A “dose-dependent” growth inhibition effect in ethanol buffer (with no EtOH in controls) spans five orders of magnitude, and shows growth rates all with overlapping confidence intervals at 95%.

Of 304 papers submitted to various open access journals, 157 were accepted, many of them without any real review taking place. 98 were rejected, and 49 were still up in the air at press time. The article seems to make a solid case against the relatively nascent open access model of publishing, and that is certainly the tone represented by the article and associated press coverage. However, if I assume that the average reader of Science is scientifically literate, then I would expect that most readers will remain unconvinced that open access is dead and dangerous.

In Who’s Afraid of Peer Review Bohannon combines language from both scientific and journalistic writing styles, taking advantage of the credibility implied by describing sample-selection and procedural decisions in a semi-scientific manner, as well as the journalist’s ability to make general claims with a strength that would be questionable in a scientific article.

Examples:

And the acceptances and rejections of the paper provide the first global snapshot of peer review across the open-access scientific enterprise.

137 of the journals chosen for this investigation were pulled from a black list maintained by Jeffrey Beall at the University of Colorado Boulder. In places (such as the general description of results) the overlap between Beall’s list and the journals selected from the DOAJ is not clear. In the original sample, 16 of these journals are in both the DOAJ and Beall’s list, but it is difficult to tell if they made it into the final analysis because 49 of the 304 journals selected for submission were thrown out for “appearing derelict” or failing to complete the article review by press time.

For the publishers on his [Beall’s] list that completed the review process, 82% accepted the paper. Of course that also means that almost one in five on his list did the right thing—at least with my submission. A bigger surprise is that for DOAJ publishers that completed the review process, 45% accepted the bogus paper.

This is somewhat misleading, as it implies that the 45% and 82% results are exclusive of each other. I could not tell just from reading the paper what proportion of the 16 journals found in both Beall’s list and the DOAJ made it to the final analysis. Furthermore, I know this is misleading based on how Jeffrey Beall, who is quite close to the subject, interpreted it: “Unfortunately, for journals on DOAJ but not on my list, the study found that 45% of them accepted the bogus paper, a poor indicator for scholarly open-access publishing overall.”

Acceptance was the norm, not the exception.

157/304 journals (51.64%) accepted the paper. While this is a majority, I would hardly qualify acceptance as a typical result when the split is so nearly even, especially when 137 of the 304 journals had already been blacklisted. Discrediting open access in general based on the results reported is not a fair conclusion.

Overall, the article just misses making a strong critical statement about the state of scientific publication, instead focusing only on problems with predatory publishing in open access. By ignoring traditional journals, we are left without a comparison to inform what may be quite necessary reform in scientific publishing. Bohannon’s article is likely to be seen and read by a large number of people in both science and scientific publishing. Editors can be expected to be on alert for the sort of fake paper used by Bohannon and Science, making any comparison to traditional publishing models just about impossible for now. Finally, the overall effect is to damn innovation in publishing, particularly open access models, and it is not surprising that the sting article was published by the “king-of-the-hill” of traditional scientific journals. It is possible that the backlash against open access and publishing innovation in general will actually impede necessary progress in scientific publishing.

As long as an academic career is judged blindly on marketing metrics such as publication frequency and researchers continue to accept excessive publication fees, there will remain an incentive for grey market “paper-mills” to gather up unpublishable papers for profit. Overall, the open access model has thus far incorporated too much from traditional publishing and not enough from the open source movement.

Science magazine warns you that open access is too open, I say that open access is not too open enough.

text in block quotes is from Who’s Afraid of Peer Review by John Bohannon, Science, Oct. 4 2013

Original version of image here

EDIT: link to John Bohannon’s article

DEAR ABBE: What’s with the “twinkle” in this Hubble image?

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the Spirit of Ernst Abbe
Legendary physicist Ernst Abbe answers your photonics questions

DEAR ABBE: I was cruising around the internet the other day in my web-rocket when I came across this stellar image of the comet ISON, taken by the Hubble space telescope. The stars appear to be twinkling. I was under the impression that the twinkling effect we see on earth is due to the atmosphere, and last time I checked the Hubble was something of a space telescope, so shouldn’t Hubble be above twinkling? -HUMBLED BY HUBBLE

DEAR HUMBLED: You’re right about twinkling, it is not apparent to observers located outside of a dense atmosphere, the topic of the 1969 paper “Importance of observation that stars don’t twinkle outside the earth’s atmosphere” by astronaut Walt Cunningham and co-author L. Marshall Libby. But twinkling is not likely to produce such picturesque points on stars as you see in that Hubble image. Rather, what appears to the naked eye as twinkling will serve to blur and smudge the image of a star in a time-averaged intensity measurement, such as a photograph.

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The spikes you see in the image in question are due to something else entirely. Twinkling stars are a result of a fickle refractive media, the atmosphere, inadvertently being included in an imaging system. The culprits causing these spikes are intentionally built into the optical system, though the effect on the image formed is a byproduct of their form rather than their primary function. What you see as four regular points oriented to the same direction on every bright star is actually the result of diffraction around the secondary mirror support struts[2][3]. Since the spikes are the Fourier transform of the struts themselves[4], they will affect every light source in the image according to their shape and brightness. The appearance of diffraction spikes is so common that the human mind essentially expects it in this type of image, and can be considered aesthetic. Ultimately, though, any light ending up in the diffraction spikes is light that could have contributed to forming the accurate image of the scene. If a dim object of interest resides by a very bright point of light, the diffraction spikes of the latter can interfere with the clear few of the dim object.

Hubble’s successor, the James Webb telescope will have three struts rather than four[5], resulting in a very different set of diffraction spikes. Not only will the James Webb struts differ in number, but these will be arranged in a sort of triangular pyramid. Diffraction around the strut will affect the final image differently at different lengths along each strut, because they will occupy a range of distances from the primary mirror. The resulting spikes should be quite interesting.

Comet ISON image available at hubblesite.org.

Do you have a question for Abbe? Ask it in the comments or tweet it @theScinder

Stop Saying Dynamical

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Following close behind experimental testing of falsifiable hypotheses, the secondary responsibility of a scientist is arguably clear communication of results. Given that the majority of research is ultimately funded by the tax-paying public, it is important that outcomes are eventually conveyed in a manner that can be understood by an intelligent layperson. Increased scientific literacy in policy makers and their constituents is a prerequisite to face modern challenges such as changing climate, public health, and the consequences of population pressure. Effective outreach to the public is more important than ever. Accepting the previous statement, why is there a continuing trend among scientists to mask communicative content through cryptic language, particularly when perfectly acceptable and widely recognized terms are available? I’ll focus on what I consider to be the most obvious and ridiculous offender, the great scourge of scientific writing, faculty information pages, and grant proposals; the great occluder of meaning, intimidator of readers, the entirely redundant bit of lexicon: dynamical.

Dynamical, like its more accessible and less attention-hungry sibling word dynamic, has its roots in the Greek dynamikos, meaning powerful. In general both terms relate to something that changes with time. Since both “dynamical” and “dynamic” function as adjectives, they are essentially interchangeable, the only difference between that I have ever been able to discern is the demographics of their use. “Dynamical” is used by physicists, mathematicians and engineers who work in dynamical systems theory, a branch of mathematics dealing with systems described by differential (if continuous) or difference (if discrete) equations. The additional suffix “-al” that delineates the two words seems to have been born of single, somewhat malicious intent: to serve as brick and mortar in the construction of an ivory tower separating scientists and small-folk. It is exactly this sort of word choice that leads to the perception that scientists have more smarts than sense and that they produce results that ultimately fail to have any application to the real world. Ultimately this serves as fuel for the anti-science fire burning through the minds of policy makers and the public. Consider the following two sentences and the impression they would leave on a reader over a morning coffee:

“We utilize the time-slice method as a means of dynamical downscaling to specify expected climate change for Southern Europe”

“We utilize the time-slice method as a means of dynamic downscaling to specify expected climate change for Southern Europe”

From:

U. Cubaschll, H. von Storch, J. waszkewitz, E. zorita. Estimates of climate change in Southern Europe derived from dynamical climate model output . Climate Research . November 29 , 1996.

Even though the sentence makes reference to specific methods that a non-specialist reader might not be familiar with, the language is descriptive enough to impart a conceptual understanding of what the authors describe, except for that cumbersome “dynamical,” which throws the whole thing into question. It reads as if it came from a humour piece poking fun at absent-minded professor types. The null-meaning suffix implies there is meaning above and beyond the root word where there is none, it just sounds more complicated. This is not an outcome that scientists should strive for, no matter how intelligent it makes them feel to use it.

As disciplines in life science become increasingly concerned with complexity and modeling, I expect the number of life scientists interested in studying dynamic systems will only continue to rise. Given the particularly relevant nature of life sciences to understanding our relationship to our living planet, I beg you, wherever possible, to avoid using the word dynamical. The physicists, mathematicians, and engineers may be entrenched in their devotion to the nonsense word, but there’s no reason for this senseless departure from clarity to infect biologists, ecologists, biochemists, etc. any more than it already has. The arbitrary and counterintuitive way that scientists name the genes they discover-a combination of sarcasm, mystery and the opposite of their function-is a big enough mess.

 

Consider this an invitation to attempt to delineate the dynamic/dynamical word pair in the comments.

Stereographic anaglyph from shift-lens

In thinking about camera arrays, integral photography, and light fields, I began to see the similarities between stereographic photos and those from an array of cameras (or a single camera occupying multiple positions at different times). What sort of depth can be achieved by a moving lens over a stationary sensor? A fair amount, for distances at which the object distance is not >> than the inter-aperture distance between lens positions. The result is below: you’ll need a red/blue pair of filters or glasses to view it. Tilt-(shift) stereograph

A perspective control lens like the one used here is typically used to straighten the “vanishing lines” of tall buildings or features without wasting sensor/film space, and generally for perspective control. The lens I used here was a 35mm f/2.8 Canon FD tilt-shift lens on a Nikon D5100 with a Fotodiox mount/infinity correction adapter, the images were separated by ten lateral ticks as marked on the lens body (these appear to be about a millimetre, but are not labeled). The object distance was approximately ten cm.

Plenoptic imaging on a macro bellows rail

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After watching Dr. Marc Levoy’s talk on light fields and the Stanford camera array I thought I’d investigate for myself the uses for synthetic aperture photography. From the talk:

By changing the amount of shift, you can change the depth of objects that are in focus. And here’s what that looks like. So we’re focusing synthetically on the bushes, across the street through my grad students into the building and there’s a step stool in the building.

This is about the same as matching up the left/right channel on a stereo anaglyph, but with more perspectives as inputs. To get a feel for things I drilled out a camera mount to attach to the end of a macro bellows rail and took a series of horizontally displaced images, shifting and combining them in Octave to focus at different depths.
Continue reading “Plenoptic imaging on a macro bellows rail”