Error when running Spot Counter in Fiji

Hi all! I receive this message when run the Spot Counter plugin in Fiji. Can somebody help?

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52u; Java 1.8.0_202 [64-bit]; Mac OS X 10.15.3; 344MB of 3977MB (8%)
 
java.lang.IllegalArgumentException: "Spot mean" column not found
	at ij.measure.ResultsTable.getValue(ResultsTable.java:392)
	at edu.ucsf.valelab.spotCounter.Spot_Counter.run(Spot_Counter.java:223)
	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:265)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114)
	at ij.IJ.runUserPlugIn(IJ.java:235)
	at ij.IJ.runPlugIn(IJ.java:196)
	at ij.Executer.runCommand(Executer.java:150)
	at ij.Executer.run(Executer.java:68)
	at java.lang.Thread.run(Thread.java:748)

Thank you!

@wevian

I believe @nicost is the best person to help you here…

I need a bit more to help. Can you share the dataset you used, and the steps you used to get to this error?

1 Like

I just used one image for the test, I have attached below.
First I transfer it to grayscale to 8 bit via image>type>8bit.
then I run the plugin, settings are these
then the error pops up.


With those settings, the plugin does not find any spots in your image and then runs into and Exception. As the documentation says, it is a really simple plugin and not all possible error conditions are checked. You need to play with BoxSize and Noise Tolerance to identify spots. Luckily, the plugin provides immediate feedback in the image itself. A BoxSize of 12, and Noise Tolerance of 40 worked reasonably well for me (note that the algorithm used works well for single molecule images, not necessarily for other things.

Thank you! It works!
However, I have another question. We stained the cells with tri-color, and we need the cells with nuclear only (blue). I want to compare the same cells under the different fluorescence light, how may I do that?

What I attached here was took in the same view. How to get rid of the yellow tiny cells without the nuclear (didn’t appear under the blue).

I don’t think that you want to use the spot counter plug. Try to formulate what you want to do as clearly as possible (for instance: I would like to find all the blue blobs and then quantify how much green there is in each blob), and post that under a new subject on this forum.

The spot counter plugin is exactly meant to do what its name implies: Count Spots :wink:

2 Likes