1063 78 15299 3 49087 document 15299 USAF.zip application/zip ac7876bcd6a2e2a976bc2a78e82cc22a MD5 76165721 2021-09-07 10:47:42 https://researchdata.bath.ac.uk/1063/1/USAF.zip 1063 1 1 application/zip other Stack of images taken on the OpenFlexure Microscope of a USAF target corner using a 40x objective. en public cc_by

USAF.zip

data 15300 3 49089 document 15300 zea.zip application/zip 59c6972585a77ee95e2246bafe97a4e7 MD5 439039989 2021-09-07 10:58:43 https://researchdata.bath.ac.uk/1063/2/zea.zip 1063 2 2 application/zip other Stack of images taken on the OpenFlexure Microscope of a zea seed using a 40x objective. en public cc_by

zea.zip

data 15304 3 49171 document 15304 tile_example.zip application/zip 3ab90c5cac2ff2e7fd992262c3b78913 MD5 4046783885 2021-09-14 12:46:45 https://researchdata.bath.ac.uk/1063/3/tile_example.zip 1063 3 3 application/zip other 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% en public cc_by

tile_example.zip

data 15305 4 49173 document 15305 smart_stack_processing.ipynb text/plain aac10d57688f66421a3dfe5a5ff8d2b2 MD5 5610 2021-09-14 13:26:05 https://researchdata.bath.ac.uk/1063/4/smart_stack_processing.ipynb 1063 4 4 text/plain other 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 en public cc_gnu_gpl

smart_stack_processing.ipynb

code 15423 2 49688 document 15423 peak_plot.ipynb text/plain ac1e0c73719677ec700d001f0b405674 MD5 31908 2021-10-14 15:22:52 https://researchdata.bath.ac.uk/1063/9/peak_plot.ipynb 1063 9 9 text/plain other 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. en public cc_gnu_gpl

peak_plot.ipynb

code 15425 3 49718 document 15425 comparison.ipynb text/plain fd69e6a02aa7c71f01efd98ab23c9228 MD5 90356 2021-10-18 11:08:36 https://researchdata.bath.ac.uk/1063/11/comparison.ipynb 1063 11 11 text/plain other 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. en public cc_gnu_gpl

comparison.ipynb

code 15426 2 49722 document 15426 requirements.txt text/plain 8258d8bcb756859504f6d644624ca983 MD5 3040 2021-10-18 13:27:28 https://researchdata.bath.ac.uk/1063/12/requirements.txt 1063 12 12 text/plain other Requirements file to allow recreation of the environment included code was written and ran in en public cc_by

requirements.txt

documentation 15428 1 49727 document 15428 indexcodes.txt text/plain c734a4da26cbee0aa7e2c464a8d4e600 MD5 4 2021-10-18 14:37:17 https://researchdata.bath.ac.uk/1063/14/indexcodes.txt 1063 14 14 text/plain other Generate index codes conversion from other to indexcodes en public

indexcodes.txt

http://eprints.org/relation/isVersionOf https://researchdata.bath.ac.uk/id/document/15426 http://eprints.org/relation/isVolatileVersionOf https://researchdata.bath.ac.uk/id/document/15426 http://eprints.org/relation/isIndexCodesVersionOf https://researchdata.bath.ac.uk/id/document/15426 15434 2 49781 document 15434 README.md text/plain 0e880dd1891a5f02c6f681df0ebab929 MD5 3545 2021-10-21 13:58:05 https://researchdata.bath.ac.uk/1063/15/README.md 1063 15 15 text/plain other README file explaining the code, data and figures associated with this archive en public cc_by

README.md

documentation archive 11016 disk0/00/00/10/63 2021-10-25 15:23:32 2025-11-15 05:53:45 2021-10-25 15:23:32 data_collection show Knapper Joe jak44@bath.ac.uk 0000-0002-5519-1700 University of Bath TRUE Supervisor Bowman Richard rwb34@bath.ac.uk 0000-0002-1531-8199 University of Bath GS0070 dept_physics microscopy, open source, focus, sharpness Full details of the collection methods, analysis and motivation are included in the associated publication. 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. 2021-10-09 University of Bath public https://gitlab.com/jaknapper/z-step-measurements Code, method and data for the z step size measurements https://doi.org/10.5281/zenodo.5564503 Archived code for performing the smart stack procedure RightsHolder University of Bath Engineering and Physical Sciences Research Council https://doi.org/10.13039/501100000266 EP/R013969/1 Detailed Malaria Diagnostics with Intelligent Microscopy Engineering and Physical Sciences Research Council https://doi.org/10.13039/501100000266 EP/R011443/1 Automated microscopy for high-throughput malaria research. Royal Society https://doi.org/10.13039/501100000288 URF\R1\180153 UR Fellowship - Robotic microscopy for globally accessible science & healthcare cent_c3bio 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. 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 en 1 10.15125/BATH-01063 https://doi.org/10.1111/jmi.13064 pub open Dataset