Searching the Algorithm Space to Automate Scientific Image Analysis Workflows

Wed 24 July 2019 by Dr. Dirk Colbry

Picture of Noah in front of her poster

Summer 2019 SROP student poster presentation at MidSure by Noah Stolz

Scientific data is often gathered in the form of Images. Scientific Image analysis is the process of pulling specific measurements out of images. Which measures are important complete depend on the scientific question being asked. For this reason, there …

read more

The Keyboard Trap: Making Jupyter Notebooks Accessible to All Students

Wed 24 July 2019 by Dr. Dirk Colbry

Picture of Abudit in front of her poster

Summer 2019 CMSE Undergraduate Intern Poster presentation at MidSure by Abudit Rai:

Jupyter Notebook is a relatively new environment that incorporates formatted text (using markdown), multimedia (video and pictures using html) and executable code where users can write and execute code within “cells” for languages such as Python, Julia, and …

read more

Surplus Tool Cabinet

Tue 09 July 2019 by Dr. Dirk Colbry

Picture of my Surplus tool Cabinet

I found this really durable whiteboard conference room cabinet at the MSU surplus store and converted it to a tool cabinet.

The original cabinet had 3/4" whiteboard panels in the back and additional panels on the inside of each door:

Whiteboard on door

These things were really heavy! I removed all of …

read more

2019 Ensure Talk - An Engineers Autobiography

Tue 25 June 2019 by Dr. Dirk Colbry

EnSURE Logo

I gave my annual autobiographical talk today to the EnSURE (Engineering Summer Undergraduate Research Experience) students. I give this talk every year and it is noticeably different that most of my presentations because the EnSURE organizers asked me to talk about myself and how I got where I am (instead …

read more

Research Team Retreat

Tue 18 June 2019 by Dr. Dirk Colbry

Research group in front of college van

This summer we managed to find a time to take my research team on a retreat (Road Trip!) to the lake (Noah, Abudit, Shelby, Lilly and Anna). It was a great opportunity to get to know each other and really bond as a team. We played games, had a boat …

read more

Workshop Community Building for High-Performance Computing Curriculum development

Mon 10 June 2019 by Dr. Dirk Colbry

National Computational Science Institute Logo

XSEDE Logo

Last year, I attended a two-and-a-half-day community and curriculum building workshop. It could not have been more perfectly timed. I was able to come up with a solid plan for my CMSE401 parallel programming course which I ended up teaching this last spring.

This year I was not able to …

read more

Do More, Faster: Utilizing Advanced Computational Resources in Your Research Team

Tue 21 May 2019 by Dr. Dirk Colbry

INSciTS Logo

Here are my slides from the SciTS conference last month.

The SciTS conference is the annual international forum dedicated to SciTS, bringing together thought leaders from a broad range of disciplines and fields, including: communications, management, social and behavioral sciences, information technology, systems science, and translational research. It provides investigators …

read more

Automating Scientific Image Analysis Workflows

Tue 23 April 2019 by Dr. Dirk Colbry

GA Title Slide

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 …

read more

Extracting Desire to learn (D2L) zip files into student folders

Mon 15 April 2019 by Dr. Dirk Colbry

D2L Logo

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 …

read more

Sphere-O-Bot (JJRobots version)

Sat 13 April 2019 by Dr. Dirk Colbry

Sphere-O Robot

So, the Sphere-O-Bot was my first (and so far only) JJRobots project a few years ago (when I didn't have a blog). My 3D printer was not in the best shape but I was able to get everything assembled and working.

I dug out the Sphere-O-bot this week and after …

read more