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 →