How is it that computers can drive cars, interpret MRI scans, and recognize our children in photographs? For decades, we hand-crafted image analysis algorithms for computers to follow. Now, we set computers loose with more general algorithms and mountains of data, and the machines learn on their own. Both of these approaches are fascinating, incorporating … Continue reading Upcoming book announcement! “How We Taught Computers To See”
About a recent paper on biological light emission. Do you emit light? The naive answer is no. None of us light up a room as we enter, other than perhaps metaphorically. The intermediate level answer, familiar to undergraduate physics majors, is yes — not by virtue of being alive but because of fundamental thermodynamics: everything … Continue reading The Bright Side of Life (Literally)
Last term (Fall 2024) I again taught the computational image analysis course I developed a few years ago (see 2021, 2022). It was again a mixed graduate and undergraduate course, this time with an enrollment of 18: 14 graduate and 4 undergraduate. For a primarily graduate elective course, this is a large number of students; … Continue reading Image Analysis Course Recap, Fall 2024
This past term, Fall 2022, I taught for the second time a course I created on image analysis. (Syllabus.) The structure and content were similar to last year’s — last year went well, and I put lots of work into it, so “if it ain’t broke…” Here’s a summary of things in the 2021 course … Continue reading Image Analysis Course Recap, Fall 2022
A more technical post than most. If the symbol and the equation look familiar to you, you’ll be fine. If not, you may still like the post, but in case you’re about to depart I’ll put my customary link to my pop-science biophysics book’s description here, and also share this week’s news that it will … Continue reading What does the Heisenberg Uncertainty Principle have to do with microscopy?
This past term (Fall 2021) I taught a course on image analysis. It was a new course — not just new for me but completely new, though it grew out of an informal image analysis class I’ve taught “off the books” before and have posted about. The class went well, though I severely underestimated how … Continue reading Image Analysis: Reflections on a New Course
About a new paper from my lab [1] on why gut bacteria swim, and whether their host cares. Many bacteria swim. It’s a great way to explore one’s surroundings, run away from toxins, or move toward regions with more food. Over the past several years, as we’ve used 3D microscopy to peer inside zebrafish to … Continue reading Putting the brakes on gut bacteria
Synopsis: In a recent paper from my lab [1], we report on watching gut bacteria get pummeled by low doses of antibiotics. The antibiotics induce changes in the spatial organization of the microbes, with major consequences for their ability to persist in the gut. Motivations At high enough doses, antibiotic drugs will kill bacteria, or at … Continue reading An intestinal amplifier for antibiotics
Synopsis: A blurb about a recent paper from my lab [1], on our discovery that the bacterium that causes cholera can manipulate the mechanical environment of an animal gut to expel resident bacteria. Introduction: cholera’s tools, and ours Cholera killed more people in the 19th century than any other epidemic disease, and it continues to … Continue reading New Tricks from an Old Bacterium
Review articles — papers that summarize a topic or a technique, assessing our present state of understanding and our hopes for the future — are useful and often enjoyable to read. In Physics, these are well respected but rather rare. In Biology, it sometimes seems like the ratio of primary articles to review articles isn’t … Continue reading The Once and Future Light Sheet
