Recent Publications

. Persistent homology for the automatic classification of prostate cancer aggressiveness in histopathology images. Medical Imaging 2019: Digital Pathology, 2019.

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. Persistent Homology for the Quantitative Evaluation of Architectural Features in Prostate Cancer Histology. Scientific Reports, 2019.

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Recent & Upcoming Talks

Introducing Shell and Basic Development on HPC Systems
Jul 19, 2018 6:00 PM

Recent Posts

A while ago my research lab acquired a new workstation, but my PI, well meaning as he is, purchased a system with an AMD GPU (FirePro W7100) rather than an Nvidia card, so CUDA is not an option. For the longest time I thought deep learning was not going to happen with TensorFlow using an OpenCV library, but I recently stumbled on a library PlaidML, a tensor compiler that allows for the use of OpenCL devices, and sits as a layer underneath common machine learning frameworks.

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Having recently needed to convert the format of an enormous quantity of images I stumbled upon GNU parallel, a powerful and simple utility for replacing shell loops with a parallel alternative. Mogrify with GNU Parallel Here is a simple example where I use GNU parallel to parallelize the conversion of a series of svs (a format commonly used for pathology images from digital whole slide scanners) to tiffs, a much more common format.

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This is a simple list of tips and tricks for the shell that I discovered over the course of many years of messing around in shell and wanted to coalesce into a single document, partly to remember, and partly to share with others. Persistent SSH Sessions In order to ensure that your SSH sessions do not get disconnected after a period of inactivity simply add the following to your .

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