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Software accompanying Lutton et al. 'Formation and closure of macropinocytic cups in Dictyostelium' (Current Biology, 2023)
Tools
Bretschneider, Till (2023) Software accompanying Lutton et al. 'Formation and closure of macropinocytic cups in Dictyostelium' (Current Biology, 2023). [Online]. (https://wrap.warwick.ac.uk/175423). Coventry, UK: University of Warwick, Department of Computer Science.
Archive (ZIP) (Software accompanying Lutton et al. 2023 (Current Biology))
Lutton 2023 Code.zip - Supplemental Material Available under License Creative Commons Attribution 4.0. Download (119Mb) |
Official URL: https://wrap.warwick.ac.uk/175423
Abstract
Code and sample data accompanying Lutton et al. "How macropinocytic cups form and close in Dictyostelium" (Current Bioloogy, 2023)
Matlab scripts require Matlab 2021b
Fiji scripts require Fiji 1.53q
Jupyter notebooks are accompanied by conda environment files encoding requirements (requires conda).
The full image analysis pipeline also uses the Curvature Enhanced Random Walker (Lutton et al. 2021,
software available at https://pilip.lnx.warwick.ac.uk/TMI_2020/),
and MiCellAnnGELo (Platt et al. 2023, software available at https://github.com/CellDynamics/MiCellAnnGELo).
Image analysis pipeline:
The pipeline input is deconvolved 5D tiff stacks, prepared for Matlab using the Fiji scripts provided.
Steps of the pipeline:
-Matlab: batch_segmentation_setup
-CERW: applied to each series (compiled as a command line tool)
-Matlab: batch_postprocess
-Matlab: batch_surface_generate
-MiCellAnnGELo: use this software to interact with and annotate the generated surfaces
-Matlab: batch_generate_patch_data
-domain_grading (jupyter notebook): Use this notebook to annotate generated patches at each time point
Scripts in code/MATLAB/measure can subsequently be used to obtain various measurements taken in the paper.
Sample data:
sample series of 5 frames are provided, with the following files:
-<series_name>_decon-<frame_range>.tif: 5D tif stack of the deconvolved
dual-channel time series of 3D images
-cell: series of corresponding dual channel surface data in .ply format
-cup_bases.csv: list of manually selected points at the base of the cups
-*_options.mat: Matlab struct containing options for each step of the pipeline
that uses Matlab
Item Type: | Digital Scholarly Resource | |||||||||
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Subjects: | Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software | |||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Computer Science | |||||||||
Publisher: | University of Warwick, Department of Computer Science | |||||||||
Place of Publication: | Coventry, UK | |||||||||
Official Date: | April 2023 | |||||||||
Dates: |
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Publication Status: | Published | |||||||||
Media of Output (format): | MATLAB ; .zip ; .xlsx ; .tif ; .mat ; .ply ; .ipynb ; .ijm | |||||||||
Access rights to Published version: | Open Access (Creative Commons) | |||||||||
Copyright Holders: | University of Warwick | |||||||||
RIOXX Funder/Project Grant: |
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