Nucleus counter in cookbook

Hi,

Even on a fresh install of ImageJ 1.51f (Fiji) after installing Cookbook, I can’t get the nucleus counter to work with any other threshold method than “Current”. Whatever I try, I get error messages like this:

Unrecognized command: “OtsuThresholding 8bit”

Unrecognized command: “k-means Clustering”

My input image is an 8bit grayscale LUT tif-file where I want to count cell nuclei.

Do I need some other plugin installed for this to work? Any help would be appreciated.

Thanks for the bug report, @matias_e!

TL;DR: I have added the missing plugins to Cookbook update site. Give it another try and let us know how it goes. Note that as of today, the Cookbook update site now requires Java 8.

In general, I would warn that many of the Cookbook plugins are very old, and it is probably worth your time to check out the Segmentation overview page and learn how to do things without the Cookbook update site.

Technical explanation: The Fiji Cookbook plugins are an adapted subset of the ones from the old MBF ImageJ collection. It turns out that some plugins necessary for certain functionality were not migrated over to the Cookbook repository, because they were not explicit compile-time dependencies of the calling plugins. This is because IJ.run calls plugins by name. So if the plugin is missing, we don’t know until runtime.

To prevent future problems, I have now done a thorough check of all places where IJ.run was used to call a plugin. Here is the complete list:

$ git grep -h 'IJ.run("' | sed 's/.*IJ.run(\("[^",]*"\).*/\1/' | sort -u
"8-bit"
"Adapative3DThreshold "
"Add..."
"Analyze Particles..."
"Convert to Mask"
"Duplicate..."
"Entropy Threshold"
"Fill"
"Grays"
"Image Calculator..."
"Invert"
"Mean..."
"Median..."
"Mixture Modeling threshold"
"Multi Measure"
"Multiply..."
"OtsuThresholding 16Bit"
"OtsuThresholding 8Bit"
"RGB Color"
"Red"
"Rename..."
"Scale Bar..."
"Spectrum"
"Subtract Background..."
"Watershed"
"k-means Clustering"

Of the above commands, the following are not part of the core ImageJ 1.x distribution:

"Adapative3DThreshold "
"Entropy Threshold"
"Mixture Modeling threshold"
"Multi Measure"
"OtsuThresholding 16Bit"
"OtsuThresholding 8Bit"
"k-means Clustering"

Of the missing commands, the following were easily extractable from the old MBF ImageJ plugins archive:

"Adapative3DThreshold "
"Entropy Threshold"
"OtsuThresholding 16Bit"
"OtsuThresholding 8Bit"

See these commits:

2 Likes