DeepBacs – Escherichia coli release from stationary phase - Bright field segmentation dataset and StarDist model

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 of an overnight culture 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 2 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>: 512 x 512 px² (106 nm / pixel), 19/15 individual frames (training/test dataset) 512 x 512 px² (106 nm / pixel), 7 regions of interest with 20 frames @ 2 min time interval (live-cell time series) <strong>Data annotation</strong>: Images were annotated using the Fiji freehand selection tool. <strong>Image preprocessing</strong>: Time series were stabilized using the Fiji plugin StackReg and the 480 x 480 px center region was cropped <strong>StarDist model</strong> The StarDist 2D model was trained from scratch for 200 epochs on 33 paired image patches (image dimensions: (512, 512 px²), patch size: (512 x 512 px²)) with a batch size of 2, 80 rays, grid size 1, 4-fold data augmentation and a mae loss function, using the StarDist 2D ZeroCostDL4Mic notebook (v 1.13) (von Chamier &amp; Laine et al., 2020). Key python packages used include tensorflow (v 0.1.12), Keras (v2.3.1), csbdeep (v 0.6.3), numpy (v 1.21.5), cuda (v 11.1.105). The training was accelerated using a Tesla K80 GPU. Model weights can be used with the ZeroCostDL4Mic StarDist 2D notebook or the Fiji StarDist plugin. <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