Mozilla Global Sprint

I am helping SUNY-Albany-CCI organize a team for the first ever Mozilla Science Lab global sprint. When: Tuesday, July 22, 2014 9:00 AM – 5:00 PM, Wednesday, July 23, 2014 9:00 AM – 5:00 PM Where: SUNY, Albany, main campus, New Business Building; Room BB 213 Why: 1.  Contribute to open science. 2. Learn skills that can be used… More →

Hacking trails and health data

The last two Saturdays I participated in “Hack for Change Albany” and “National Trails Day”.  Most people would consider trail work and computer programming to be very different, but both events were actually very similar in format.  Groups of volunteers got together for a common cause.  In each case we were loosely organized by a leader but also encouraged to… More →

Link Dump

Some interesting articles from the last couple of weeks…(If you follow the open science and reproducible research communities you have probably already seen these). Nate Silver comments on a repeatable data controversy.   Silver reaches a very large audience so people outside the open data community will read this.  He also makes a good point “be skeptical of the skeptics” too!… More →

ISBI 2014 Grand Challenge

Last month I attended ISBI 2014 in Beijing as part of the Deconvolution Grand Challenge.  These challenges are very important as they encourage cross fertilization of technology. The top 3 entries were. Ferreol Soulez – Learn 2D, Apply 3D Method David Biggs – Olympus Cellsens Deconvolution Software- (Very fast.  Dave did his PhD in algorithm acceleration). Sander Kromwijk –   A… More →

ImageJ2-GPU Deconvolution

I’ve just added an ImageJ2 wrapper to YacuDecu (by Bob Pepin) in both the main deconvolution project and RogueImageJPlugins.   RogueImageJPlugins is a place where I am putting cool self contained plugins and examples.   Yacu Decu was written as an Imaris plugin.  The Imaris version can be found here. I’ve played with it a little and got about a 10x speed… More →

Simple ITK – ImageJ2 integration

As part of my larger deconvolution project I tested some of the ITK deconvolution algorithms.   It was fairly easy to integrate Simple ITK into ImageJ2 using Eclipse in an Ubuntu development environment.   Though I haven’t attempted the non-trivial task of creating distributable libraries.  I was really impressed at how simple it was to create an image processing plugin using ImageJ2… More →

Malyasian Flight 370 and Particle Detection

Image processing algorithms for microscopy are often tested on tiny round particles such as some type of metallic particles in electron microscopy or fluorescent particles in light microscopy.   In 3 dimensional imaging, the 3rd dimension is often stretched.  So when you take a picture of something spherical, it will be elongated in the 3rd dimension. We can use image processing… More →