Dataset for "Robotic microscopy for everyone: the OpenFlexure Microscope"

This dataset contains microscopy images collected to demonstrate imaging capabilities of the OpenFlexure Microscope. Images for bright-field transmission and reflection, polarisation contrast, and fluorescence imaging are provided. A set of images obtained from a large tile scan are provided, along with the Microsoft Image Composite Editor file used for tiling.

Keywords:
microscopy, open source, instrumentation
Subjects:
Optics, photonics and lasers

Cite this dataset as:
Collins, J., Knapper, J., Bowman, R., 2020. Dataset for "Robotic microscopy for everyone: the OpenFlexure Microscope". Bath: University of Bath Research Data Archive. Available from: https://doi.org/10.15125/BATH-00734.

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Data

ofm-2019-dataset.zip
application/zip (2GB)
Creative Commons: Attribution 4.0

Creators

Joel Collins
University of Bath

Joe Knapper
University of Bath

Richard Bowman
University of Bath

Contributors

Joram Mduda
Data Collector
Ifakara Health Institute

University of Bath
Rights Holder

Documentation

Data collection method:

Images were collected using the OpenFlexure Microscope as documented in the associated mansuscript.

Technical details and requirements:

Images are in JPEG format. The .spj file is a project file for use with Microsoft Image Composite Editor v2.0 (https://www.microsoft.com/en-us/research/product/computational-photography-applications/image-composite-editor/). Python scripts are written for Python v3.6+ and require non-standard libraries matplotlib, Numpy, opencv-python, picamera, PIL, pytest, scipy, and scikit-image, all of which are available from the Python Package Index (https://pypi.org/). The analysis script `run_analysis.sh` requires a global installation of the Python library micat (https://gitlab.com/bath_open_instrumentation_group/micat). It may be executed directly by a UNIX-like shell, but the command invocation it contains may be used on other platforms.

Additional information:

Additional documentation is provided within the ZIP file.

Documentation Files

README.md
text/plain (1kB)
Creative Commons: Attribution 4.0

Funders

Engineering and Physical Sciences Research Council (EPSRC)
https://doi.org/10.13039/501100000266

GCRF - Open Lab Instrumentation
EP/P029426/1

Engineering and Physical Sciences Research Council (EPSRC)
https://doi.org/10.13039/501100000266

Detailed Malaria Diagnostics with Intelligent Microscopy
EP/R013969/1

Engineering and Physical Sciences Research Council (EPSRC)
https://doi.org/10.13039/501100000266

Automated microscopy for high-throughput malaria research.
EP/R011443/1

UR Fellowship - Robotic microscopy for globally accessible science & healthcare
URF\R1\180153

Robotic microscopy for globally accessible science and healthcare
RGF\EA\181034

Publication details

Publication date: 23 March 2020
by: University of Bath

Version: 1

DOI: https://doi.org/10.15125/BATH-00734

URL for this record: https://researchdata.bath.ac.uk/id/eprint/734

Related articles

Collins, J. T., Knapper, J., Stirling, J., Mduda, J., Mkindi, C., Mayagaya, V., Mwakajinga, G. A., Nyakyi, P. T., Sanga, V. L., Carbery, D., White, L., Dale, S., Jieh Lim, Z., Baumberg, J. J., Cicuta, P., McDermott, S., Vodenicharski, B. and Bowman, R., 2020. Robotic microscopy for everyone: the OpenFlexure microscope. Biomedical Optics Express, 11(5), p.2447. Available from: https://doi.org/10.1364/BOE.385729.

Contact information

Please contact the Research Data Service in the first instance for all matters concerning this item.

Contact person: Richard Bowman

Departments:

Faculty of Science
Chemistry
Physics

Research Centres & Institutes
Centre for Nanoscience and Nanotechnology
Centre for Photonics and Photonic Materials