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 →

Noncirculant deconvolution and a simple simulation

This weekend I’m going to be giving a talk at the SUNY Albany Open Source Festival.  The talk will focus on work I’ve done using open source for the ISBI Deconvolution Grand Challenge.  Part of the talk presents a simple simulation showing the benefits of noncirculant deconvolution. The phantom I used for this test is here The non-circulant convolution is… More →

Using the ImageJ2 Framework for the 3D Deconvolution Grand Challenge

I’ve recently participated in the Second International Challenge on 3D Deconvolution Microscopy.   The challenge was described as follows. The idea of the challenge is to make the participants follow a reasonably complete deconvolution workflow, with several hurdles that are representative of real situations. These hurdles may include algorithm selection, PSF-inaccuracy compensation, noise-model calibration and regularization-parameter adjustment. My submission focused… More →

Stellaris FISH dataset #1 Deconvolution tests

Recently George McNamara, of M.D. Anderson Cancer Center posted some datasets and invited the community to share deconvolution results (description here) and compare to results he generated using a GPU algorithm.  The experiments below are done using a cropped version of the “GM 20131101Fri_StellarisFISH_1_w43 = Cy3 -N3” set. (cropped version can be downloaded here: ) Figure 1. shows an XY… More →