DeepBacs – Escherichia coli bright field segmentation dataset

Training and test images of live <em>E. coli</em> cells imaged under bright field for the task of segmentation. Additional information can be found on this github wiki. The example shows a bright field image of live <em>E. coli </em>cells and the manually annotated segmentation mask. <strong>Data type</strong>: Paired bright field and segmented mask images <strong>Microscopy data type</strong>: 2D bright field images recorded at 1 min interval <strong>Microscope</strong>: Nikon Eclipse Ti-E equipped with an Apo TIRF 1.49NA 100x oil immersion objective <strong>Cell type</strong>: <em>E. coli</em> MG1655 wild type strain (CGSC #6300). <strong>File format</strong>: .tif (8-bit) <strong>Image size</strong>: 1024 x 1024 px² (79 nm / pixel), 19/15 individual frames (training/test dataset) 1024 x 1024 px² (79 nm / pixel), 9 regions of interest with 80 frames @ 1 min time interval (live-cell time series) <strong>Image preprocessing</strong>: Raw images were recorded in 16-bit mode (image size 512 x 512 px² @ 158 nm/px). Images were upscaled with a factor of 2 (no interpolation) to enable generation of higher-quality segmentation masks. Two sets of mask images are provided: RoiMaps for instance segmentation using e.g. StarDist or binary images for CARE or U-Net. <br> <strong>Author(s)</strong>: Christoph Spahn^1,2, Mike Heilemann^1,3 <strong>Contact email</strong>: [e-mail] <strong>Affiliation(s)</strong>: 1) Institute of Physical and Theoretical Chemistry, Max-von-Laue Str. 7, Goethe-University Frankfurt, 60439 Frankfurt, Germany 2) ORCID: 0000-0001-9886-2263 3) ORCID: 0000-0002-9821-3578