Automating Scientific Image Analysis Workflows
Tue 23 April 2019 by Dr. Dirk Colbry
I was asked to give a talk to Michael Murillo machine learning seminar group. Michael put the group together as a first step to gather topics/ideas for a graduate level machine learning class that CMSE will be teaching in the fall.
In this talk I introduced a difficult machine learning problem in the area of Exploratory Image Analysis. I explained why this problem is unique and not easily solved using machine learning. Then I introduced my ideas on how we plan to try and solve the problem this summer using machine learning and, more specifically, Genetic Algorithms.
Extracting Desire to learn (D2L) zip files into student folders
At MSU we use Desire to Learn for our classroom content management system. Students can go to D2L to get their assignments and turn in their assignments though the D2L dropbox.
When grading, I can download all of the student's submissions into a zip file such as the following:
Part …
Sphere-O-Bot (JJRobots version)
Accessibility of Jupyter for Impaired Individuals
This poster presents work by CMSETech Intern, Ahsa Shekar and her work on finding ways to make Jupyter More accessible.
Abstract
Jupyter is an open-source programming environment that uses "literate programming" by combining documentation, coding and visualization into one file format. The Jupyter notebook format is also particularly well-suited for …
read moreThe challenges of developing research tools in active and responsive open source communities
This poster presents work by Professorial Assistance, Ty Buckly and Hattie Pimentel and their work on building an image annotation system inside of Jupyter.
Abstract
Scientists often gather observations of the world using images and need efficient image annotating tools to extract data from these images. Project Insight seeks to …
read moreHPCC SLURM Buy-in Notes
This year, the HPCC moved over to SLURM. Overall, I think the new scheduler is nice but it required me to relearn a bunch of things I have gotten to know by reflex.
One nice new feature is that I can manage our own Buy-in account. The CMSE department has …
read moreUnderstanding Research Technology Support and Where it Fails
I was invited to give a talk to a newly formed IT Research Support group here on MSU campus. As the name suggests, the purpose of this group is to find the best ways to help researchers use technology to do their science.
This talk was a patchwork of many …
read moreManaging Files on the MSU Engineering Jupyterhub server
The MSU Engineering Jupyterhub server provides 2GB of disk storage space for each student. It can be helpful to learn some disk management so you can use this space effectively.
For example, pip install uses a temporary folder when downloading packages. Periodically, deleting this folder can significantly free up space …
read moreVirtual Reality Talk at the MSU Library
A few weeks ago I was asked by Terence O'Neill to give a talk to the VR/AR seminar group being held at the library. He wanted me to talk about our "Mobile beast" and show how we are using VR equipment in CMSE.
The VR equipment had a bug …
read moreQuick Makefile Overview
A former student recently emailed me asking for a good reference about makefiles. To be honest, I teach a lot about makefiles but I am not sure I have a go-to source. I could have googled something but instead I just tapped out this quick description. I thought …
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