Dataset for Fast, high precision autofocus on a motorised microscope: Automating blood sample imaging on the OpenFlexure Microscope

Example images and analysis code to support the development and publication of a smart stack procedure to use closed loop movements in an autofocus procedure. Includes examples on how images can be processed and tiled, analysed to find the focal plane, and stacks tested to find the distribution of sharpest images within stacks across a large scan or collection of scans.

Keywords:
microscopy, open source, focus, sharpness
Subjects:
Medical and health interface

Cite this dataset as:
Knapper, J., 2021. Dataset for Fast, high precision autofocus on a motorised microscope: Automating blood sample imaging on the OpenFlexure Microscope. Bath: University of Bath Research Data Archive. Available from: https://doi.org/10.15125/BATH-01063.

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Data

USAF.zip
application/zip (76MB)
Creative Commons: Attribution 4.0

Stack of images taken on the OpenFlexure Microscope of a USAF target corner using a 40x objective.

zea.zip
application/zip (439MB)
Creative Commons: Attribution 4.0

Stack of images taken on the OpenFlexure Microscope of a zea seed using a 40x objective.

tile_example.zip
application/zip (4GB)
Creative Commons: Attribution 4.0

An example of the data generated by a smart stack scan, ready to be processed and tiled. Images are of a thick blood sample, taken on the OpenFlexure Microscope using a 100x oil immersion objective. For tiling, approximate overlap is 30%

Code

smart_stack_processing.ipynb
text/plain (5kB)
Software: GNU GPL 3.0

Jupyter notebook to take a completed smart stack folder and create a folder containing only the central images, ready to be tiled using Fiji distribution of ImageJ. Used to prepare images for Figure 7

peak_plot.ipynb
text/plain (31kB)
Software: GNU GPL 3.0

Jupyter notebook to produce histograms of the position of sharpest images in stacks produced by different focus methods. The underpinning images used are not included, but the results are included here as an example and to allow the notebook to plot. Used to produce Figure 8.

comparison.ipynb
text/plain (90kB)
Software: GNU GPL 3.0

Jupyter notebook to plot the JPEG and Laplacian sharpnesses of a z-stack of images. Users can use their own images or the example images used in the paper, manually judging a focused range. To recreate Figures 3 and 5, zea.zip and USAF.zip are required. The path in the fourth cell should be changed to the input folder (either `zea/8` or `USAF/11` assuming `zea.zip` and `USAF.zip` are extracted into the corresponding folders). The focused range is manually specified in the fifth cell.

Code, method and data for the z step size measurements

Archived code for performing the smart stack procedure

Creators

Joe Knapper
University of Bath

Contributors

Richard Bowman
Supervisor
University of Bath

University of Bath
Rights Holder

Documentation

Data collection method:

Standard OpenFlexure optics calibration was performed before collecting images to improve the reliability of movements in x-y, and to improve the lens shading across each image.

Technical details and requirements:

All images collected on an OpenFlexure Microscope. The OpenFlexure software version used for this development is archived at https://doi.org/10.5281/zenodo.5541934 Written in Python 3.8.2, with requirements given by requirements.txt

Additional information:

Full details of the collection methods, analysis and motivation are included in the associated publication.

Documentation Files

requirements.txt
text/plain (3kB)
Creative Commons: Attribution 4.0

Requirements file to allow recreation of the environment included code was written and ran in

README.md
text/plain (3kB)
Creative Commons: Attribution 4.0

README file explaining the code, data and figures associated with this archive

Funders

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 (The Royal Society)
https://doi.org/10.13039/501100000288

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

Publication details

Publication date: 9 October 2021
by: University of Bath

Version: 1

DOI: https://doi.org/10.15125/BATH-01063

URL for this record: https://researchdata.bath.ac.uk/id/eprint/1063

Related papers and books

Knapper, J., Collins, J. T., Stirling, J., McDermott, S., Wadsworth, W. and Bowman, R. W., 2021. Fast, high‐precision autofocus on a motorised microscope: Automating blood sample imaging on the OpenFlexure Microscope. In: Journal of MicroscopyWiley. Available from: https://doi.org/10.1111/jmi.13064.

Contact information

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

Contact person: Joe Knapper

Departments:

Faculty of Science
Physics

Research Centres & Institutes
Centre for Biosensors, Bioelectronics and Biodevices (C3Bio)