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 →

I am no expert in internet security.  I am also fairly new to open source so I don’t claim to understand all the complicated factors that led to the heartbleed bug.  From what I understand the problem occurred because of a bug in a piece of widely used open source code.  There is quite a bit of discussion on heartbleed… More →

So I just posted my first dataset on figshare.  This is really cool.   Figshare that is.  Well the simulation too.  Even though it is simple.   It is a simulation that reproduces a bead image that Kurt Thorn of UCSF shared with me.  The actual image is here.   And the deconvolved of the actual image here.   I did the… More →

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 →

Saturday March 29th I attended the SUNY Albany Open Source Festival.  The highlight for me was a talk by Marcus D. Hanwell called “Saving Science: Open or bust”.    I haven’t been able to track down the video for the OSF version of his talk.  But the TEDx version of the talk (Saving Science: Open or Perish) is here…    

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 →