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.
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.
Export
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
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.
Methodology link:
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), 2447. Available from: https://doi.org/10.1364/boe.385729.
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
Royal Society
https://doi.org/10.13039/501100000288
UR Fellowship - Robotic microscopy for globally accessible science & healthcare
URF\R1\180153
Royal Society
https://doi.org/10.13039/501100000288
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 papers and books
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), 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
Faculty of Science
Chemistry
Physics
Research Centres & Institutes
Centre for Nanoscience and Nanotechnology
Centre for Photonics and Photonic Materials
