First-time Fiji user, trouble initiating Kalman Stack Filter


I’m just starting to use Fiji for analyzing my microscopy data. I am trying to utilize the Kalman stack filter (image --> stacks --> Kalman Stack Filter) to reduce the noise in my images. It seems like clicking on the KSF is supposed to open a dialogue box where one can set parameters. Yet, when I click KSF, I get a dialogue asking me to specify a file location. I’m not understanding whether it needs me to locate the KSF plugin, or specify a save location (hopefully I wouldn’t have to do this for every image stack). No one in my lab has run into this problem before, so any help is appreciated! I am running a Mac circa late 2012, OS X El Capitan. Java is up to date.

Hi @Jillian_Liu,

welcome to the forum! :slight_smile:

I just a had quick look at the source code of the plugin. It does not operate on the active image but asks for a folder that contains the file(s) and a pattern that all files that shall be processed have in common. You can, for starters, select the file you had opened previously in the file chooser that pops up and continue…


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