There has been growing interest in reproducible research. The interest arises from the idea that scientific discoveries that are one off, isolated and never to be repeated have limited value. For research to inform future science other must be able to reproduce the results. There are even courses on reproducible research. However, a look at the courses and a quick search of PubMed will reveal that when people refer to reproducible research, they often mean shared data or shared analytic code. And when I write “shared data”, I don’t even really mean any data, I mean electronic data … a spreadsheet, a database, etc. Of course, the Methodology section of journal articles are supposed to support reproducible research, but these are often hints and teasers for what was done, rather than a genuine “how to”.
Reproducibility becomes more challenging when all one has to work with is a one-off observation. How do I show you what I saw? The question became particularly relevant to me in a recent discussion with a colleague about reproducible microscopy. The obvious answer is, “a photograph” — and with a professional set up, one can achieve spectacular results — but what should be done in resource poor settings where money and equipment are limited?
I am one of the investigators on a Wellcome Trust funded “Our Planet Our Health” award led by Rebekah Brown at the Monash Sustainable Development Institute. The “Revitalisation of Informal Settlements and their Environment” (RISE) study involves the collection of large quantities of diverse data from informal settlements in Makassar, Indonesia and Suva, Fiji. Most of the samples will be collected by in-country teams, and they will not have access to high-end equipment. Nonetheless, some of the samples will have to be examined under a microscope in Makassar and Suva. It is likely that we will have to rely on basic equipment and Lab Technicians with limited skills in microscope photography. From my SEACO experience, I would be looking for a low-cost solution that can be implemented with basic training. The solution “works” if the images are appropriate; that is, they are the thing of scientific interest, and are of sufficient fidelity that a researcher somewhere else in the world can interpret them appropriately. It is not necessary for the technician to be brilliant, just adequate.
I decided to play. I am neither a good photographer nor am I good at microscopy. I reasoned that if I could get something approximating a reasonable image, then a Lab Technician with some actual training would have no problems. The best low-cost camera solution is not to buy another piece of equipment at all. We are already committed to using a smartphone/Tablet solution in the RISE project and plan to use them for capturing photographs, tagging photographs, and uploading them to a server. The only challenge was getting the smartphone camera to “peek” into the microscope. Fortunately, there is a broad range of solutions, and I opted for the very cheapest I could find on eBay. It cost me USD$5.99, brand new, including postage and handling.
The mount is straightforward to use, although my first attempt was pretty awful. I found a weevil crawling around the kitchen (welcome to the tropics!) and that became the first portraiture subject.
The images are of much higher resolution than I have posted here. I didn’t know what I was doing, and most of the image is taken up with the microscope surrounds rather than the subject of the photograph. I tried the next day, this time using a peppercorn as the subject — it didn’t move as quickly.
The only real difference in my approach was that this time I zoomed in slightly on the peppercorn. I will never look at peppercorns the same way. What appears to be (to my unqualified eyes) fungal mycelium is less than appealing. Nonetheless, it also seems like the general approach to capturing microscope images might be a reasonable. As long as the technician knows what to photograph, the quality of the images is almost certainly good enough for others to view and interpret. This is potentially quite exciting because it does allow science (and quite basic science) to be virtual and shared. A photograph of a microscopic image taken in Makassar could be shared with the world within hours giving scientists anywhere an opportunity to look, think, interpret, question and suggest.