Deconvolution using ImageJ/Fiji

plugin

#1

I’ve been experimenting with the “Parallel Iterative Deconvolution” plugin for ImageJ on Macs running OSX 10.12 (at work) and 10.14 (at home). The plugin appears to run fine under ImageJ v1.52i, but it won’t launch under Fiji (which I would prefer to use). Any ideas?


#2

Hi @jmhallADP

Are you getting an error message?? If so post it, and perhaps it will give us a clue.

If you are looking to use “Parallel Iterative Deconvolution” specifically, you could contact the author and ask about the issue https://imagej.net/Parallel_Iterative_Deconvolution.

If you are looking for a general deconvolution plugin you could try DeconvolutionLab2. It has a wide variety of algorithms and a interactive GUI.

If you have an NVIDIA card on your Mac or access to Windows or Linux OS you could also consider imagej-ops, which has an experimental fast implementation of the Richardson Lucy algorithm (it is a modified version of YacuDecu). The drawback of this approach is that it is geared towards scripts (No interactive GUI, only a very simple GUI) and probably requires some wrangling to get it working on a Mac (see this thread).


#3

Hi Brian,

Thanks for your reply! I tried using DeconvolutionLab2, but didn’t get very good results with it. The Parallel Iterative Deconvolution algorithm was easier to use and produced impressive results (at least under ImageJ v1.52i). I’ll follow up on your suggestion and try contacting the author about the issue with Fiji (no error message there – it shows up in the list of plugins, but just doesn’t launch).

Thanks again,

Jim


#4

Solution found in another thread (http://imagej.1557.x6.nabble.com/Parallel-Iterative-Deconvolution-td5013104.html). Move jtransforms-2.4.jar out of jars folder and it launches just fine.