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Mask out TetraSpeck beads with nuclear regions #400

Closed
Tracked by #403
vreuter opened this issue Dec 6, 2024 · 0 comments · Fixed by #428
Closed
Tracked by #403

Mask out TetraSpeck beads with nuclear regions #400

vreuter opened this issue Dec 6, 2024 · 0 comments · Fixed by #428
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enhancement New feature or request
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vreuter commented Dec 6, 2024

@TLSteinacker

We will lose some extra beads by extending a 2D nuclear mask throughout the full depth / along the full z-axis, but no big deal since usually we have plenty of legitimate bead spots. Furthermore, extending the $xy$ mask to 3D by simply translating it along $z$ prevents us from biasing our pool of beads, from which we select for drift correction and accuracy assessment, towards regions in which $z$ slices are disproportionately not occupied by a nucleus.

Needed to prevent mistaking a spot from FISH or IF for a fiducial bead

@vreuter vreuter added the enhancement New feature or request label Dec 6, 2024
@vreuter vreuter added this to the v0.12 milestone Dec 6, 2024
@vreuter vreuter self-assigned this Dec 6, 2024
@vreuter vreuter modified the milestones: v0.12, v0.13 Dec 12, 2024
@vreuter vreuter changed the title Mask out TetraSpeck beads with nucler regions Mask out TetraSpeck beads with nuclear regions Feb 17, 2025
vreuter added a commit to vreuter/looptrace that referenced this issue Feb 19, 2025
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