Fiji logo

A group working over in Plant and Soil Sciences are experts on ImageJ but are relatively new to the HPCC. Together we put together a workflow for getting ImageJ up and running on the HPCC.

Step 1: Log onto the HPCC with an X11 connection

Log onto the HPC using an X11 connection. You need x11 in order to test the install using the Graphical User Interface (GUI). If you are on windows, I recommend MobaXTerm as an easy way to get started, if you are on Mac you may need to install XQuarts.

If you don't have X11 working you can try logging in using the HPCC remote server and a "full linux desktop" by going to the following website:

https://webrdp.hpcc.msu.edu

You can test if graphics are working by typing the following on the command line:

xeyes

Step 2: Install ImageJ

For this step I recommend installing Fiji (Fiji is just ImageJ) which a little easier to use than ImageJ proper. For one thing it makes installing a few plug-ins much easier.

Download the 64-bit installer into your home directory on the HPCC. Go to the Fiji website to get a URL link to the latest version. Once you have the URL you can run the following command on an HPC Development node:

wget https://downloads.imagej.net/fiji/latest/fiji-linux64.zip

After the file has downloaded you just need to unzip the file using the following command:

unzip fiji-linux64.zip

Test ImageJ using the following command:

~/Fiji.app/ImageJ-linux64

The first time running it will ask if you want to run the "updater." I would recommend doing this.

Step 3: Install needed plugins

Once you have Fiji running you shold be able to install most plugins from the user interface. You can also copy plugin jar files to the plugins folder inside the Fiji.app folder.

Step 4: Write a Macro

You can run for about 2 hours on any of the HPCC development nodes, however, to really take advantage of the HPCC you want to run in batch mode. Batch mode does not let you use the mouse and click on the graphics which means you need to create an ImageJ macro that runs from start to end without any user input. For now I will assume that you know how to make a macro, if not, you may have to look for some sort of online tutorial or read the manual,

If you want to just do a quick test I recmmend making a macro with just a "hello world" print command as follows:

print(hello world);

Save the file as myMacro.ijm

Step 5: Submit the macro to the scheduler

Let us assume that your macro name is myMacro.ijm then the following submission script should work to get your macro running in SLURM:

#!/bin/bash
#SBATCH --mem=4gb
#SBATCH --time=04:00:00
#SBATCH -n 1
#SBATCH -c 1

module load java
module load powertools

srun ~/Fiji.app/ImageJ-linux64 --headless --memory=4000M -macro myMacro.ijm

js $SLURM_JOB_ID

If we call the above script runFiji.sb then you can submit the job to the SLURM scheduler using the following command:

sbatch runFiji.sb

That should be it. You can change the required memory or the amount of time it takes to run.


CMSE Presentation at SC19

Sun 17 November 2019 by Dr. Dirk Colbry

SC19 Logo

I just got out of giving a presentation about the CMSE department as part of the Sixth SC Workshop on Best Practices for HPC Training and Education (BPHTE19) workshop at SC19. It was fun to show people what we are doing in CMSE and share our progress. Here is a …

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Sherpas of Supercomputing

Sun 15 September 2019 by Dr. Dirk Colbry

Cover picture of the September 2019 ASEE PRISM Magazine Featuring the Sherpas of Supercomputing article

I had the honor of recently being featured in an ASEE PRISM Magazine article about research facilitation.

An essential, if not yet well-defined, field is emerging at the intersection of research and the high-performance machines that make sense of big data. By Lucy Birmingham and Mark Matthews

See the full …

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Developing curriculum to train Graduate students how to utilize Raspberry Pis to Automate Research Labs

Wed 24 July 2019 by Dr. Dirk Colbry

Picture of Shelby in front of her poster

Summer 2019 CMSE CMSE Undergraduate Intern Poster presentation at MidSure by Shelby Santos

Raspberry Pis (RPis) are affordable microcomputers (approx. $35) that have the capability to revolutionize the accuracy and efficiency of data collection in basic laboratory environments. Recreationally, RPis can be used as a base for smart televisions, home …

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Investigation of the process of converting a C++ code into an implementable FPGA file

Wed 24 July 2019 by Dr. Dirk Colbry

Picture of Ana in front of her poster

Summer 2019 ENSURE Student Poster presentation at MidSure by Ana Flavia Borges de Almeida Barreto

A Field Programmable Gate Arrays (FPGAs) is an integrated circuit that can be “rewired” to become other circuits. This ability makes FPGAs highly configurable and can significantly help speed up large scale computation used in …

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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 …

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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 …

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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 …

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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 …

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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 …

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