My development class also has a lab. The last few weeks have all been teaching them how to get good optics on a research scope, and how to take photomicrographs with my PixeLink camera system. Today I’m going to show them how to appropriately process an image for publication, so they’ll learn a few digital enhancement tricks and a few ethical rules. I lay down a few laws about using image processing on scientific data:

What you must do to your image:

• You must archive the original data and work with a copy. If I ask to see the original after you’ve enhanced the image up the wazoo, you better be able to show it.

• You must document every step and every modification you make. You’re going to describe everything either on the image itself or in a figure legend; if this were to be published, you’d probably include it in the Methods section.

• You must explain the scale and orientation of the image. The scale is usually shown by including a scale bar; orientation may be shown either by including annotations (text describing landmarks in the image) or an explanation in the figure legend, such as that it is a sagittal or horizontal section.

• You must save the image in a lossless format, such as .png or .psd or .tiff. Do not save it in a lossy format like .jpeg, which can add compression artifacts.

What you may do to your image:

• You may crop and rotate the image.

• You may adjust the contrast and brightness for the whole image.

• You may carry out simple enhancements, like applying a sharpening filter or unsharp masking, to the whole image…but remember, document everything!

• You may splice multiple images together to produce a photomontage; you can also insert panels with enlarged or otherwise enhanced regions of the image, as long as it is absolutely clear what you’ve done.

What you may not do to your image:

• You must not carry out selective modifications of portions of the image; you cannot sharpen the cell you care about and then reduce the contrast for other regions, for instance. You should not burn or dodge regions of the image.

• No pixel operations or retouching: you are not allowed to go into the image and paint your data into existence!

We do a lot of this preliminary basic stuff because I run the course out of my research lab, rather than a student lab. I want to make sure they’re not going to break anything, and also that they know how to do good imaging, a skill they’ll find useful in other courses and in research (years ago when I taught this stuff, we’d also do black&white darkroom work — nobody does that any more, so now it’s all photoshop). The goal is to get them all able to churn out lovely photographic data, so later I can just hand them some nematodes or fruit fly embryos and tell them to do their own experiments and observations, just show me the pretty pictures when they’re done.

It’s a good life, being able to sit back and let students bring me gifts of biological beauty. I think they’ll also be posting some of these to their blogs.

I was bad. I didn’t post my summary last week, so this is actually what I taught a week ago and what I taught today.

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This is an abbreviated summary of my class lecture in developmental biology today. This was the first day of class, so part of the hour was spent on introducing ourselves and going over the syllabus, but then I gave a lightning fast overview of the history of developmental biology.

Classical embryology began with Aristotle, whose work was surprisingly good: he approached the problem of development with relatively few preconceptions and fairly accurately summarized what was going on in the development of the chick. Most of this old school embryology is descriptive and was really a narrow subset of anatomy, but there were a few major conceptual issues that concerned the old investigators, in particular the question of preformation (the plan of the embryo is laid out in the egg) vs. epigenesis (the plan of the embryo emerges progressively). Aristotle, by the way, was on the right side of this debate, favoring epigenesis.

In the 19th century, development was seen as a progressive process that paralleled the hierarchical organization of nature — that is, developmental biology, what there was of it, was coupled to the great ladder of being. This is not an evolutionary idea, but reflects the view that there was a coherent pattern of greater and lesser development that was part of a coherent divine plan for life on earth. The German ‘Natural Philosophers’ pursued this line of reasoning, often to degrees that now look ridiculous in hindsight. In contrast, there were developmental biologists like Karl Ernst von Baer who wanted nothing to do with a cosmic teleology but instead preferred to emphasize observation and data, and simple minimal hypotheses.

In the late 19th century, developmental biology split into two directions. One was a dead end; Ernst Haeckel basically lifted the explanatory framework of the natural philosophers, replaced divinity with evolution, and tried to present development as a parallel process to evolution. Von Baer had already demolished this approach, and despite a few decades of popularity Haeckelian recapitulation died as a credible framework for studying evolution in the early years of the 20th century. The other direction developmental biology took was Wilhelm Roux’s Entwicklungsmechanik, or experimental embryology. This was an approach that largely eschewed larger theoretical frameworks, and focused almost exclusively on observation and experimental manipulation of embryos. It was a successful discipline, but also divorced mainstream developmental biology from the evolutionary biology that was increasingly influential.

As examples of Entwicklungsmechanik, I discussed Roux’s own experiments in which he killed one cell in a two-cell embryo and saw partial embryos result, an observation that fit with a preformationist model, but more specifically a mosaic pattern of development, in which patterns of development were encoded into the cytoplasm or cortex of the egg. Those experiments were seriously flawed, however, because the dead cell was left attached to the embryo, and could have deleteriously affected development. The experiments of Hans Driesch were cleaner; he dissociated embryos at the four cell stage, cultured each blastomere independently, and discovered that each isolated cell developed fully into a complete, miniature larva.

Driesch, unfortunately, interpreted these results to imply that there was an entelechy, or guiding intelligence outside the embryo, and that the only conceivable explanation was the existence of purpose behind embryology. This was also a dead end; the modern explanation for the phenomena is that they regulated, that is, that cells determine their fate by interacting with one another, rather than some kind of cosmic plan. And that’s really going to be a major focus of this course: how do cells communicate with one another, how are genes regulated to set up coherent and consistent patterns of gene expression that produce the organized cell types we find in an adult multicellular plant or animal?

That set up the next lecture. Entwicklungsmechanik, while representing a solid and productive research program, quickly reached its limits, because what we really needed to examine were those patterns of gene expression rather than trying to infer them from observations of morphology. The big breakthrough was the melding of developmental biology and molecular biology — most of the modern developmental biology literature focuses on examining interactions between genes. So on Wednesday we’ll get another fast overview of the molecular genetics research program, and a bit of evo-devo.

Slide thumbnails (PDF)