BACKGROUND: Large image datasets acquired on automated microscopes typically have some fraction of low quality, out-of-focus images, despite the use of hardware autofocus systems. Identification of these images using automated image analysis with high accuracy is important for obtaining a clean, unbiased image dataset. Complicating this task is the fact that image focus quality is only well-defined in foreground regions of images, and as a result, most previous approaches only enable a computation of the relative difference in quality between two or more images, rather than an absolute measure of quality. RESULTS: We present a deep neural network model capable of predicting an absolute measure of image focus on a single image in isolation, without any user-specified parameters. The model operates at the image-patch level, and also outputs a measure of prediction certainty, enabling interpretable predictions. The model was trained on only 384 in-focus Hoechst (nuclei) stain images of U2OS cells, which were synthetically defocused to one of 11 absolute defocus levels during training. The trained model can generalize on previously unseen real Hoechst stain images, identifying the absolute image focus to within one defocus level (approximately 3 pixel blur diameter difference) with 95% accuracy. On a simpler binary in/out-of-focus classification task, the trained model outperforms previous approaches on both Hoechst and Phalloidin (actin) stain images (F-scores of 0.89 and 0.86, respectively over 0.84 and 0.83), despite only having been presented Hoechst stain images during training. Lastly, we observe qualitatively that the model generalizes to two additional stains, Hoechst and Tubulin, of an unseen cell type (Human MCF-7) acquired on a different instrument. CONCLUSIONS: Our deep neural network enables classification of out-of-focus microscope images with both higher accuracy and greater precision than previous approaches via interpretable patch-level focus and certainty predictions. The use of synthetically defocused images precludes the need for a manually annotated training dataset. The model also generalizes to different image and cell types. The framework for model training and image prediction is available as a free software library and the pre-trained model is available for immediate use in Fiji (ImageJ) and CellProfiler.

Direct-threaded interpreters use indirect branches to dispatch bytecodes, but deeply-pipelined architectures rely on branch prediction for performance. Due to the poor correlation between the virtual program's control flow and the hardware program counter, which we call the context problem, direct threading's indirect branches are poorly predicted by the hardware, limiting performance. Our dispatch technique, context threading, improves branch prediction and performance by aligning hardware and virtual machine state. Linear virtual instructions are dispatched with native calls and returns, aligning the hardware and virtual PC. Thus, sequential control flow is predicted by the hardware return stack. We convert virtual branching instructions to native branches, mobilizing the hardware's branch prediction resources. We evaluate the impact of context threading on both branch prediction and performance using interpreters for Java and OCaml on the Pentium and PowerPC architectures. On the Pentium IV our technique reduces mean mispredicted branches by 95%. On the PowerPC, it reduces mean branch stall cycles by 75% for OCaml and 82% for Java. Due to reduced branch hazards, context threading reduces mean execution time by 25% for Java and by 19% and 37% for OCaml on the P4 and PPC970, respectively. We also combine context threading with a conservative inlining technique and find its performance comparable to that of selective inlining.

Dynamic program optimization is increasingly important for achieving good runtime performance. A key issue is how to select which code to optimize. One approach is to dynamically detect traces, long sequences of instructions spanning multiple methods, which are likely to execute to completion. Traces are easy to optimize and have been shown to be a good unit for optimization. The paper reports on a new approach for dynamically detecting, creating and storing traces in a Java virtual machine. We first describe four important criteria for a successful trace strategy: good instruction stream coverage, low dispatch rate, cache stability, and optimizability of traces. We then present our approach based on branch correlation graphs. A branch correlation graph stores information about the correlation between pairs of branches, as well as additional state information. We present the complete design for an efficient implementation of the system, including a detailed discussion of the trace cache and profiling mechanisms. We have implemented an experimental framework to measure the traces generated by our approach in a direct-threaded Java VM (SableVM) and we present experimental results to show that the traces we generate meet the design criteria.

This paper reports on a new approach to solving a subset-based points-to analysis for Java using Binary Decision Diagrams (BDDs). In the model checking community, BDDs have been shown very effective for representing large sets and solving very large verification problems. Our work shows that BDDs can also be very effective for developing a points-to analysis that is simple to implement and that scales well, in both space and time, to large programs.The paper first introduces BDDs and operations on BDDs using some simple points-to examples. Then, a complete subset-based points-to algorithm is presented, expressed completely using BDDs and BDD operations. This algorithm is then refined by finding appropriate variable orderings and by making the algorithm propagate sets incrementally, in order to arrive at a very efficient algorithm. Experimental results are given to justify the choice of variable ordering, to demonstrate the improvement due to incrementalization, and to compare the performance of the BDD-based solver to an efficient hand-coded graph-based solver. Finally, based on the results of the BDD-based solver, a variety of BDD-based queries are presented, including the points-to query.