PySTACHIO: Python Single-molecule TrAcking stoiCHiometry Intensity and simulatiOn, a flexible, extensible, beginner-friendly and optimized program for analysis of single-molecule microscopy data

As camera pixel arrays have grown larger and faster, and optical microscopy techniques ever more refined, there has been an explosion in the quantity of data acquired during routine light microscopy. At the single-molecule level, analysis involves multiple steps and can rapidly become computationally expensive, in some cases intractable on office workstations. Complex bespoke software can present high activation barriers to entry for new users. Here, we redevelop our quantitative single-molecule analysis routines into an optimized and extensible Python program, with GUI and command-line implementations to facilitate use on local machines and remote clusters, by beginners and advanced users alike. We demonstrate that its performance is on par with previous MATLAB implementations but runs an order of magnitude faster. We tested it against challenge data and demonstrate its performance is comparable to state-of-the-art analysis platforms. We show the code can extract fluorescence intensity values for single reporter dye molecules and, using these, estimate molecular stoichiometries and cellular copy numbers of fluorescently-labeled biomolecules. It can evaluate 2D diffusion coefficients for the characteristically short single-particle tracking data. To facilitate benchmarking we include data simulation routines to compare different analysis programs. Finally, we show that it works with 2-color data and enables colocalization analysis based on overlap integration, to infer interactions between differently labelled biomolecules. By making this freely available we aim to make complex light microscopy single-molecule analysis more democratized.

Research activities of faculty in academic departments of medicine

To assess the involvement of current medical faculty in research, a research activities questionnaire and a faculty roster form were sent to all full-time, salaried faculty of departments of medicine in medical schools in the United States. Valid responses from 7483 faculty members were received from 119 medical schools. About 88% of respondents are men; 83% have M.D. degrees; 8% have a Ph.D. degree; and 7% have both degrees. Twenty-four percent of the faculty who have done research had little preparation for a research career. However, 45% of faculty with M.D. degrees had 2 or more years of research training. Seventy-seven percent of faculty with only an M.D. degree reported research activity from 1982 to 1983; the median effort of all faculty with an M.D. is 25%. Faculty with both degrees are more involved in research and the median effort for those with a Ph.D. is 95%.