Hello I'm using ImageJ to analyse -czi and -zvi files. I'm using an automatic selection with "create selection" or "analyze particle"s. It's working well when openening/importing the files with ImageJ. But when I try to use the Bio-Format importer Plugin with the same pictures, it's not working. Not my intended ROIS are selected but the background or even nothing. With using the plugin something about the parameters of the picture changes and I don't know what it is or how to undo it. Does somebody has an idea?
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The [_Create Selection_](http://imagej.nih.gov/ij/docs/guide/146-27.html#sub:Create-Selection) command creates a selection from a **thresholded image** or a binary mask. Are you sure you are using the same thresholds? – Jan Eglinger May 03 '15 at 16:44
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yes, tried it with the same files and the same thresholds several times. – Nathalie May 03 '15 at 16:45
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One of the Solutions I realised is a Change of scale. My original files use pixels, whereas the BioFormat importer converts the scale into microns.
Analyze--> Set Scale... --> Click to remove scale or changing the scale solves one part of the problem.
For a macro following code restores the scale:
run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
Still somethng about the colour values changes, I can't find, create selection is still not working properly.
Nathalie
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