Re: Microscope Image Focus Quality plugin

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Re: Microscope Image Focus Quality plugin

Just in case other people are interested in use of this plugin I have received the email below from Samuel Yang (see below) and the plugin works now as advertised when installed according to

However, be aware that the plugin fails if the Stardist plugin is also installed. I guess there is a problem with duplicated file names but have not had a look at this.

Best wishes


From: Samuel Yang <[hidden email]>
Sent: 14 May 2020 19:03
To: [hidden email] <[hidden email]>; Straatman, Kees (Dr.) <[hidden email]>
Subject: FIJI microscope image focus quality plugin fixed


Curtis sent me your discussion here:
Bad URL Removed - see why ->

Thanks for letting us know the model download link was broken, it should be fixed now.

Just a quick comment -- if you're finding the best-focus image in a z-stack, looking at simple statistics like the standard deviation of pixels in a slice is a robust and fast way.

But assessing image focus on a single image in isolation (without z-stacks, or without a large example dataset of in and out-of-focus images) is a harder task that we approached with our model:<>

PDF of paper:<>

It is slow, but you can choose to compute the measure on fewer tiles within an image:

Hope this helps. Feel free to share this response on the mailing list, I'm not sure how to post to it.

Samuel Yang

ImageJ mailing list:

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