Single cell annotations in 3D bacterial biofilms of Vibrio cholerae

This dataset comprises both 3D raw microscopy images and corresponding 3D label images, in which each cell has been annotated,. The annotation was performed either using a semi-manual annotation scheme, or a fully manual annotation, as indicated in the file names. The semi-manual annotation data is available for 5 different biofilm colonies of Vibrio cholerae (biofilm_1, biofilm_2, biofilm_3, biofilm_4, biofilm_5). The fully manual annotation was performed on a sub-region of "biofilm_1". For this sub-region of biofilm_1 a semi-manual annotation is also available. The image resolution is as follows: z-resolution = 100 nm. xy-resolution: 65nm/px. Images were acquired using a spinning disk confocal microscope (Nikon Ti-E with Yokogawa CSU), equipped with a silicon oil 100x (NA 1.35, Olympus) objective, and an EMCCD camera (Andor iXon Ultra 888). The cells express a superfolder-GFP in the cytoplasm, which was excited using a 488nm laser. The V. cholerae strain that was used has the designation KDV613. Further information about this dataset is available in the associated journal publication, with title "Single-cell segmentation in bacterial biofilms with optimized convolutional neural networks enables tracking of cell lineages and measurements of growth rates".