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Spot Z position is not set in Roi Manager #6

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CellKai opened this issue Apr 26, 2021 · 0 comments
Open

Spot Z position is not set in Roi Manager #6

CellKai opened this issue Apr 26, 2021 · 0 comments

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@CellKai
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CellKai commented Apr 26, 2021

Hi, I noticed that when adding the spot ROIs to the Roi Manager, their Z-position is not set explicitly, which can lead to this information getting lost in some cases, see related image.sc forum thread: https://forum.image.sc/t/rois-added-to-roi-manager-by-macro-do-not-maintain-all-properties/37533/5

Example issue: Run RS fish including"add ROIs to RoiManager", then save the image using Bio-Formats as ome.tif including the ROIs.

This issue can be solved by setting the spots z positions explicitly by adding a line in RS-FISH/src/main/java/gui/Radial_Symmetry.java after line 344

imp.setSliceWithoutUpdate( 1 + (int)Math.round( spot.getDoublePosition( 2 ) ) );

e.g.: p.setPosition( 1 + (int)Math.round( spot.getDoublePosition( 2 ) ) );

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