Dataset for "Closing the loop in open-source microscopy: Automated focus, scanning, image tiling and resolution calibration on the OpenFlexure Microscope"

This dataset contains calibration images used to test the performance of a microscope.

Data for the thesis "Closing the loop in open-source microscopy: Automated focus, scanning, image tiling and resolution calibration on the OpenFlexure Microscope". The dataset consists of two image collections:

- a collection of sets of images for tiling and stitching together, used to test the effectiveness of a Python tiling program;
- a collection of aligned edge images used to assess the resolution of a microscope.

Subjects:

Mechanical engineering

Robotics and Autonomy

Tools, technologies and methods

Medical Instrumentation, Devices and Equipment

Cite this dataset as:
Knapper, J., 2023. Dataset for "Closing the loop in open-source microscopy: Automated focus, scanning, image tiling and resolution calibration on the OpenFlexure Microscope". Bath: University of Bath Research Data Archive. Available from: https://doi.org/10.15125/BATH-01278.

Export

Data

tiling_archive.zip
application/zip (10GB)
Creative Commons: Attribution-Share Alike 4.0

The input images used for the tiling chapter of the associated thesis, excluding the images contributing to blood scan

resolution.zip
application/zip (4GB)
Creative Commons: Attribution-Share Alike 4.0

The images used for the resolution chapter of the associated thesis, split by the objective used

IHI_blood.zip
application/zip (2GB)
Creative Commons: Attribution 4.0

Images contributing to blood scan

Code

openflexure … tching_bd1e0797.zip
application/zip (305kB)
Software: GNU GPL 3.0

Tiling and stitching code

auto_mtf.zip
application/zip (509kB)
Software: GNU GPL 3.0

Code for collecting LSF images from a USAF resolution target

micat.zip
application/zip (490kB)
Software: GNU GPL 3.0

Code for extracting the LSF from a scan of slanted hard edges

The set of images contributing to blood scan is under embargo until it has been published separately by data collection researchers at IHI.

GitLab repository for tiling and stitching code

GitLab repository for auto_mtf (collecting LSF images from a USAF resolution target)

GitLab branch for usafcal extension to Micat (extracting the LSF from a scan of slanted hard edges)

Creators

Joe Knapper
University of Bath; University of Glasgow

0000-0002-5519-1700

Contributors

University of Bath
Rights Holder

Documentation

Data collection method:

The images were all collected automatically on the OpenFlexure Microscope, as described in the respective chapters of the linked thesis, using the included tiling and stitching code and the Bath Open Instrumentation Group's Micat resolution code.

Technical details and requirements:

Please see the Micat documentation for its technical requirements. The included code requires Python 3.8+ and the packages listed in `requirements.txt`.

Additional information:

The tiling and stitching code included here corresponds to commit bd1e0797 in the Git repository. The auto_mtf code corresponds to commit 73c62c44. The code for the usafcal extension to Micat corresponds to commit 4b7aeed3.

Methodology link:

Stirling, J., and Collins, J., 2020. Micat: Microscopy Calibration and Testing using USAF resolution targets. GitLab. Available from: https://gitlab.com/bath_open_instrumentation_group/micat.