deepthought: the microscopy acquisition stack as an object of study

Analysis-in-the-loop microscopy has been demonstrated many times, but it is rarely used outside the laboratories that build it. Each demonstration constructs its own acquisition infrastructure, so little transfers between them, and it has remained unclear which parts of the problem are already solved. In this work, the microscopy acquisition stack was itself treated as the object of study, and was investigated by construction. A minimal stack was built end to end, and four applications were then driven through it as test conditions. These were fixed-cell high-throughput immunofluorescence, live time-lapse imaging of an unsynchronized population, fluorescence anisotropy imaging, and autonomous focus and exposure. Each element of the stack was then classified by how it varied across these applications. Device access, sequencing, data storage and viewing held constant, and mature implementations of each were adopted unchanged. Interpretation, or how an image becomes a set of entities, differed with the application and belongs behind an interface. Two elements had nothing available to adopt and were therefore built. These are a geometric representation of the sample that a plan can traverse, and a representation of a run that yields detected objects rather than images. With those two in place, feedback from analysis into acquisition was ordinary control flow. The system was applied to the DNA damage response, where 22,000 cells were acquired and analyzed without operator intervention, and cells were followed through mitosis over 24 hours in an unsynchronized population without chemical synchronization. One element, targeting, or the choice of where to observe next, varies between applications and remains unabstracted in this implementation. It is identified here as the next requirement. Codehttps://github.com/ndsystems/deepthought (acquisition client), https://github.com/ndsystems/hard-link (instrument access server)