ImageJ macro result table (2D Gaussian Fitting)

[reddyg]

Hi,

I'm trying to use a ImageJ.1x plugin via KNIP's IMageJ1 macro node. I'm mostly interested in the Results Table from this macro (not the image output). When I do run the KNIP ImageJ1 Macro node it executes fine but I'm not getting the output from the results table. There isn't much in the KNIME log (even under DEBUG mode).

Any thoughts?

Additional Details:

In the KNIP ImageJ Macro node, I selected "Pure Code" and added the following:

run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel global");
run("Find Maxima...", "noise=500 output=[Point Selection]");
run("GaussFit OnSpot", "shape=Circle fitmode=[Levenberg Marquard] rectangle=4 pixel=100 max=500 cpcf=1 base=0");

 

About ImageJ Plugin:

The plugin I'm using is from the following URL. This plugin does a 2D Gaussian fitting of diffraction limited emitters/spots.

https://imagej.nih.gov/ij/plugins/gauss-fit-spot/index.html

KNIME ImageJ Configuration:

I've configured the ImageJ plugin path in the KNIME preferences correctly to a local installation of Fiji (NOT the default path from KNIP).

Installation Details:

KNIME 3.2.1, 64-bit Windows 7, JRE 8.x 

KNIME Image Processing    1.5.3.201610200657 

KNIME Image Processing - ImageJ Integration (Beta)    0.11.2.v201610060929 

[christian.birkhold]

Hi Reddy,

Any chance you can provide a small example workflow indicating the problem? This would help me a lot debugging your code!!

Thanks!

Christian

[reddyg]

Hi Christian -

I'm attaching simple workflow. Hope it helps to troubleshoot the issue.

 

Best,

 

Reddy

• gaussian_fitting_imagejmacro.knwf

[christian.birkhold]

Hi Reddy,

thanks for the workflow. That helped a lot.

I think I found a way to make this possible. The problem is that not all ImageJ1 plugins are implemented for batch execution. In this particular case we are lucky and can't workaround the problem. I hope this helps,

Christian

PS: Nightly build is currently building for your. Fix should be available in 1 hour.

PPS: Parallelization unfortunately doesn't help you with IJ1 macros.. IJ1 batch execution can't be parallelized on a single JVM.

 

[reddyg]

Hi Christian -

 

Thanks for the quick fix for fetching the table from ImageJ1's Results Manager. Also, appreciate the pointer about the parallelization for IJ1's macro execution.

Any chance of getting 2D Gaussian Fitting for single molecule location microscopy?

 

Best,

 

Reddy