Making science (part II): The making of a scientist

Former postdoc fellow Svend Kjaer has today published his first first-author paper after leaving the lab. It has appeared online at the Nature Structure and Molecular Biology website. He’s got the first glimpse of the three-dimensional structure of the extracellular domain of the RET receptor, giving insights into how it binds ligand and how its mutation causes disease. Something we were striving to see for several years while he was at our lab has now been achieved and it’s one of the great success stories of making science. It took a lot of perseverance, a good measure of ingenuity and the crucial guidance and support of Svend’s current mentor and common friend Neil McDonald from the CRUK institute in London. As if by coincidence, from Svend comes also this link to the one-hour film “Naturally Obsessed: The Making of a Scientist” telling the story of three graduate students in a crystallography lab at Columbia University, NYC and their road to success (or failure) through “years of trial and error and unflinching dedication”. It gives good insights into real science making in a lab, the elusive thrill of its ups and downs, and what it takes to get to the finish line. Link from the picture above.

Capturing RAW

I am often asked why I shoot my photographs in RAW format. RAW capture refers to the direct transfer of the information acquired by the sensor of a digital camera to the memory card without any in-camera processing. In the 18-megapixel Canon EOS 7D, this translates into files of 25MB, compared to the 6MB of a high-resolution JPG-compressed file. Why would one like to shoot RAW files? The RAW format contains all the information captured by the sensor and is therefore most amenable to corrections of exposure, saturation, chromatic aberrations and noise during post-processing. Compressed JPG files contain a reduced amount of information and so are much more limited to adjust during post-processing. Why would someone want to adjust a photograph? Shown below are three examples taken during a recent trip to the Otavalo valley in Northern Ecuador. In all cases, the top image is straight-out-of-camera, while the lower image is after conversion in Adobe CS4 Camera Raw (no Photoshop in any of these examples!).


With the early afternoon sun blazing over these beautiful mountains at the feet of the Imbabura and a very bright sky, the top image straight-out-of-camera is flat and lacks clarity and contrast. The sky is overexposed, detail in the clouds is lost, the different tones of greens in the foregorund do not come out as they looked in reality. There is also uneven exposure across the frame. In the second image, all this is corrected. This picture has vibrant colors, even exposure in foreground and background and detail in the clouds. Comparison of the histograms before (left) and after (right) also reveals these differences:

The highlights are clipped (outside of range) in the first histogram but tamed in the second, which also has a more even distribution of tones.

This awesome wide-angle view of the flooded crater of Cuicocha was taken at the wide end of a 10-22mm EF-S lens aided with a circular polarizer B+W filter. The filter did a good job at taming reflections on the lake, giving a deep beautiful blue color to the water. But the top image lacks pop, the clouds are overexposed, and the greens in the foreground are wahsed out. The lower image shows the lake in all its glory, even under such an intense midday sun. A comparison of the histograms before (left) and after (right) tells the story:

Highlights are now better resolved (although some clipping persists) and the tones show a much nicer dynamic range.

This last image was taken at the Cascada del Peguche, a small but very beautiful waterfall near Otavalo. (But… you ought to watch out for those tiny mosquitoes; they are truly deadly!) Here, some small rapids downstream the river called for a long exposure to show off the flowing water. The photograph was taken handheld with a Canon EOS 7D and the100mm 2.8 IS L macro lens at 1/5 second and f/25 (barely open!). At 1/5 sec exposure, image stabilization came really in handy here! The shadows on the left image have no detail, it can barely be made up what’s below those stones on the upper left and bottom right. Neither the grass or the water shine as they should (and did!). On the right, the water is pure silk and the shadows have detail and pop. Much better contrast as well. OBS! no polarizer was used here. (I still need to get a 67mm polarizer for this new lens.) The compressed shadows of the original show very clearly in the left histogram:

All those clipped dark pixels (left) are now back and resolved very nicely (right).

Why capturing RAW? The conversions shown here would have been much more difficult to obtain from in-camera JPG files. On the other hand, the disadvantages are larger files, hence the requirement of bigger memory cards and disk space, and post-processing time at the computer. As the examples above illustrate, the results are well worth the extra effort.