Fluorescent Neuronal Cells is a dataset for instance segmentation, semantic segmentation, and object detection tasks. It is used in the neurobiological research.

The dataset consists of 283 images with 5533 labeled objects belonging to 1 single class (stained neuron).

Images in the Fluorescent Neuronal Cells dataset have pixel-level instance segmentation annotations. Due to the nature of the instance segmentation task, it can be automatically transformed into a semantic segmentation (only one mask for every class) or object detection (bounding boxes for every object) tasks. There are 50 (18% of the total) unlabeled images (i.e. without annotations). There are no pre-defined train/val/test splits in the dataset. The dataset was released in 2021 by the University of Bologna, Italy.

Fluorescent Neuronal Cells is under CC BY-SA 4.0 license.

Source

If you make use of the Fluorescent Neuronal Cells data, please cite the following reference:

@unpublished{amsacta6706,
  title = {Fluorescent Neuronal Cells},
  note = {Unpublished},
  year = {2021},
  publisher = {University of Bologna},
  keywords = {semantic segmentation; object detection; object counting; neuronal cells; fluorescent microscopy},
  author = {Clissa, Luca and Morelli, Roberto and Squarcio, Fabio and Hitrec, Timna and Luppi, Marco and Rinaldi, Lorenzo and Cerri, Matteo and Amici, Roberto and Bastianini, Stefano and Berteotti, Chiara and Lo Martire, Viviana and Martelli, Davide and Occhinegro, Alessandra and Tupone, Domenico and Zoccoli, Giovanna and Zoccoli, Antonio},
  url = {https://amsacta.unibo.it/id/eprint/6706/},
  abstract = {By releasing this dataset, we aim at providing a new testbed for computer vision techniques using Deep Learning. The main peculiarity is the shift from the domain of "natural images" proper of common benchmark dataset to biological imaging. We anticipate that the advantages of doing so could be two-fold: i) fostering research in biomedical-related fields - for which popular pre-trained models perform typically poorly - and ii) promoting methodological research in deep learning by addressing peculiar requirements of these images. Possible applications include but are not limited to semantic segmentation, object detection and object counting. The data consist of 283 high-resolution pictures (1600x1200 pixels) of mice brain slices acquired through a fluorescence microscope. The final goal is to individuate and count neurons highlighted in the pictures by means of a marker, so to assess the result of a biological experiment. The corresponding ground-truth labels were generated through a hybrid approach involving semi-automatic and manual semantic segmentation. The result consists of black (0) and white (255) images having pixel-level annotations of where the stained neurons are located. For more information, please refer to Morelli, R. et al., 2021. Automating cell counting in fluorescent microscopy through deep learning with c-ResUnet. Scientific reports, (in press). https://doi.org/10.1038/s41598-021-01929-5. The collection of original images was supported by funding from the University of Bologna (RFO 2018) and the European Space Agency (Research agreement collaboration 4000123556).}
}

Source

Dataset Fluorescent Neuronal Cells can be downloaded in Supervisely format:

As an alternative, it can be downloaded with dataset-tools package:

pip install --upgrade dataset-tools

… using following python code:

import dataset_tools as dtools

dtools.download(dataset='Fluorescent Neuronal Cells', dst_dir='~/dataset-ninja/')

Make sure not to overlook the python code example available on the Supervisely Developer Portal. It will give you a clear idea of how to effortlessly work with the downloaded dataset.

The data in original format can be downloaded here.