Published October 5, 2021 | Version v1
Dataset Open

DeepBacs – S. aureus SIM prediction dataset and CARE model

  • 1. Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal

Description

Training and test images of live, membrane-labeled S. aureus cells for prediction of SIM super-resolution images from widefield images, as well as a trained CARE model.

Additional information can be found on this github wiki.

The example image shows a widefield fluorescence image and SIM reconstruction of Nile Red labelled, live S. aureus cells.

 

Training and test dataset

Data type: Paired microscopy images (fluorescence) of low (widefield) and high resolution (SIM)

Microscopy data type: Fluorescence microscopy (Nile Red)

Microscope:  GE HealthCare Deltavision OMX system (with temperature and humidity control, 37°C) equipped with an Olympus 60x 1.42NA Oil immersion objective and 2 PCO Edge 5.5 sCMOS cameras (one for DIC, one for fluorescence)

Cell type: S. aureus strain JE2 grown under agarose pads

File format: .tif (16-bit for widefield images and 32-bit for SIM reconstructions)

Image size: 1024 x 1024 px² (40 nm/px)
Image preprocessing: S. aureus widefield images were scaled with a factor of 2 to match the SIM reconstruction pixel size. 

 

CARE model

The CARE 2D model was generated using the ZeroCostDL4Mic platform (Chamier et al., 2021). It was trained from scratch for 300 epochs on 9400 paired image patches (image dimensions: (1024 x 1024 px²), patch size: (80 x 80 px²), 100 patches/image) with a batch size of 8 and a laplace loss function, using the CARE 2D ZeroCostDL4Mic notebook (v 1.12). Key python packages used include tensorflow (v 0.1.12), Keras (v2.3.1), csbdeep (v 0.6.1), numpy (v 1.19.5), cuda (v 10.1.243). The training was accelerated using a Tesla P100GPU and data was augmented by a factor of 4 using rotation, flipping and random zoom.

Model weights can be used with the ZeroCostDL4Mic CARE 2D notebook or the CSBDeep Fiji plugin.

 

Author(s): Pedro Matos Pereira1,2, Mariana Pinho1,3

Contact email: pmatos@itqb.unl.pt and mgpinho@itqb.unl.pt

 

Affiliation

1) Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal

2) ORCID: https://orcid.org/0000-0002-1426-9540

3) ORCID: https://orcid.org/0000-0002-7132-8842

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A_S.aureus_SIM_examples.png

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