Nuclear Boundary Annotation for 3D Imaging

Experienced bioimage analysts drew outlines around nuclear boundaries on each slice of the 3D images and labeled background regions in a different color with GIMP (https://www.gimp.org), an open-source drawing and annotation software. These annotated layers were then exported from GIMP as an image. This outline image is converted to 3D objects via a CellProfiler pipeline (https://github.com/CellProfiler/tutorials/tree/master/Annotation), and an object label matrix image is exported, in which each object’s voxels are assigned a unique integer value. These label images are referenced as ground truth.

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McQuin C., Goodman A., Chernyshev V., Kamentsky L., Cimini B.A., Karhohs K.W., Doan M., Ding L., Rafelski S.M., Thirstrup D., Wiegraebe W., Singh S., Becker T., Caicedo J.C, & Carpenter A.E. (2018). CellProfiler 3.0: Next-generation image processing for biology. PLoS Biology, 16(7), e2005970.

Publication 2018

Gimp Tree

Corresponding Organization : Allen Institute for Cell Science

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Protocol cited in 112 other protocols

Variable analysis

independent variables

Researchers manually drew outlines around nuclear boundaries on each slice of the 3D images

dependent variables

Annotated layers exported from GIMP as an image
Object label matrix image exported, in which each object's voxels are assigned a unique integer value

control variables

Background regions labeled in a different color with GIMP

Annotations

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