Description

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".

Resources

Name	Format	Description	Link
	0		http://data.europa.eu/88u/dataset/oai-zenodo-org-7035286
	0		http://data.europa.eu/88u/dataset/oai-zenodo-org-7035286
	0		http://data.europa.eu/88u/dataset/oai-zenodo-org-7035286
	0		http://data.europa.eu/88u/dataset/oai-zenodo-org-7035286
	0		http://data.europa.eu/88u/dataset/oai-zenodo-org-7035286
	0		http://data.europa.eu/88u/dataset/oai-zenodo-org-7035286
	0		http://data.europa.eu/88u/dataset/oai-zenodo-org-7035286
	0		http://data.europa.eu/88u/dataset/oai-zenodo-org-7035286
	0		http://data.europa.eu/88u/dataset/oai-zenodo-org-7035286
	0		http://data.europa.eu/88u/dataset/oai-zenodo-org-7035286
	0		http://data.europa.eu/88u/dataset/oai-zenodo-org-7035286
	0		http://data.europa.eu/88u/dataset/oai-zenodo-org-7035286
	0		http://data.europa.eu/88u/dataset/oai-zenodo-org-7035286
	0		http://data.europa.eu/88u/dataset/oai-zenodo-org-7035286

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