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ZENODO
Dataset . 2021
License: CC BY
Data sources: Datacite
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ZENODO
Dataset . 2021
License: CC BY
Data sources: Datacite
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DeepBacs ��� Bacillus subtilis fluorescence segmentation dataset

Authors: Holden, S��amus; Conduit, Mia;

DeepBacs ��� Bacillus subtilis fluorescence segmentation dataset

Abstract

Training and test images of live B. subtilis cells expressing FtsZ-GFP for the task of segmentation. Additional information can be found on this github wiki. The example shows the fluorescence widefield image of live B. subtilis cells expressing FtsZ-GFP and the manually annotated segmentation mask. Data type: Paired fluorescence and segmented mask images Microscopy data type: 2D widefield images (fluorescence) Microscope: Custom-built 100x inverted microscope bearing a 100x TIRF objective (Nikon CFI Apochromat TIRF 100XC Oil); images were captured on a Prime BSI sCMOS camera (Teledyne Photometrics) Cell type: B. subtilis strain SH130 grown under agarose pads File format: .tiff (8-bit) or .png (8-bit) For segmented masks, binary masks are used for training of CARE/U-Net models, 8-bit .tif ROI maps for training of StarDist models and .png images for training of pix2pix models Image size: 1024 x 1024 px�� (Pixel size: 65 nm) Image preprocessing: Images were denoised using PureDenoise and resulting 32-bit images were converted into 8-bit images after normalizing to 1% and 99.98% percentiles. Images were manually annotated using the Labkit Fiji plugin Author(s): Mia Conduit1,2, S��amus Holden1,3 Contact email: Seamus.Holden@newcastle.ac.uk Affiliation: 1) Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, NE2 4AX UK 2) ORCID: 0000-0002-7169-907X Associated publications: Whitley et al., 2021, Nature Communications, https://doi.org/10.15252/embj.201696235

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Keywords

Segmentation, Deep Learning, Bacteria, B. subtilis, ZeroCostDL4Mic, Fluorescence

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