Re: [Ifeffit] selection of pixels by criteria

Hi all, I use ImageJ with the ScatterJ and ScatterJn plugins to do this type of analysis of XRF maps. https://openresearchsoftware.metajnl.com/articles/10.5334/jors.89/ https://onlinelibrary.wiley.com/doi/abs/10.1111/jmi.12187 Cheers, Will Dr William W. Bennett Senior Lecturer Environmental Futures Research Institute School of Environment and Science Griffith University Gold Coast, Queensland, Australia M +61 401 186 488 w.bennett@griffith.edu.amailto:w.bennett@griffith.edu.auu Assistant Professor Nordcee, Department of Biology University of Southern Denmark Odense, Denmark M +45 8193 8111 wbennett@biology.sdu.dkmailto:wbennett@biology.sdu.dk ________________________________ From: Matthew Marcus Sent: Friday, 22 November 2019 6:33 am To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] selection of pixels by criteria A suggestion: Make a scatterplot available, plotting the pixel-by-pixel values of any two relevant quantities, and make it possible to define a polygon mask on that scatterplot. That often allows separation of chemically-distinct areas. Sincerely, Matthew Marcus On 11/21/2019 12:26 PM, Matt Newville wrote:

HI Troy,

Sorry for the late reply -- I think this sort of slipped off my radar screen.

On Sat, Nov 16, 2019 at 2:09 PM E. Rasbury mailto:troy.rasbury@stonybrook.edu> wrote:

I have used larch some for XRF maps. I like the feature for defining ROI's and then looking at the statistics of the data. I have some samples that are an intimate mix of two or more phases and I would like to extract pixels based on a criteria- like high Sr or low Fe, etc, from across a whole map region. I wonder if this feature is available, or would be easy to create on larch?

Like you say, this is not currently available in the Mapviewer GUI. But it's a good suggestion and might be possible to do with a small amount of code.

Would it work for you to say "Make an Area with all pixels where Sr Counts is above some value"? I think that would be easy to generalize from "Sr Counts" to "Ratio of ROI Counts" (or "analyzed concentration" once I get that done - a work in progress). If that's right, I think it would be "not hard to add".

--Matt

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