Data: An Injectable Meta-biomaterial: From Design and Simulation to In-vivo Shaping and Tissue induction

Dataset supporting the manuscript "An Injectable Meta-biomaterial: From Design and Simulation to In-vivo Shaping and Tissue induction" by the authors of this dataset.

Where to start

This Zenodo repository contains both raw data and runnable code for the manuscript "An Injectable Meta-biomaterial: From Design and Simulation to In-vivo Shaping and Tissue induction". The runnable code is best executed directly at CodeOcean (https://doi.org/10.24433/CO.6934377.v1). Alternatively, CodeOcean capsules are Docker images and can be run locally after download and unzipping. The full CodeOcean capsule is stored here as "CodeOceanCapsule_Injectable_meta_biomaterial.zip", it contains all the information and data to full reproduce the evaluation underpinning the manuscript " An Injectable Meta-biomaterial: From Design and Simulation to In-vivo Shaping and Tissue induction".

Quantitative raw data, in the form of text files, Excel files and R-data files useful for the data evaluation are included in "CodeOceanCapsule_Injectable_meta_biomaterial.zip". As especially the numerical simulation files are rather voluminous (100GB), we also provide a copy of the capsule without this large part, which however otherwise remains runnable for most evaluations ("CodeOceanCapsule_Injectable_meta_biomaterial_no_raw_simulation.zip"), and, for lightweight documentation of the code section only "CodeOceanCapsule_Injectable_meta_biomaterial_code_only.zip". The results of a capsule run are also provided, as "CodeOceanCapsule_Injectable_meta_biomaterial_results_run_4899036.zip".

Besides archival of the CodeOcean evaluation capsule, this repository contains additional imaging data from which some of the quantitative data treated in the CodeOcean capsule was extracted, and additionally raw files for the illustrative figures in the manuscript. This data is contained in the files "Raw_images_For_Figure_1.zip", "Raw_images_For_Figure_3.zip", "Raw_images_For_Figure_4.zip"; "Raw_images_For_Figure_5.zip", "Raw_images_For_SFigure_S6.zip", "Raw_images_For_SFigure_S8.zip", "Raw_images_For_SFigure_S9.zip", "Raw_images_For_SFigure_S19.zip".

External dependencies

To facilitate centralized software development and installation, custom R and Python libraries used by the CodeOcean capsule "CodeOceanCapsule_Injectable_meta_biomaterial.zip" are hosted on Github, with releases archived in separate Zenodo repositories. These libraries are included automatically during the build phase of the CodeOcean capsule.

This concerns the Python discrete particle simulation particleShear (DOI: 10.5281/zenodo.4589212), and the R packages textureAnalyzerGels (for analysis of mechanical compression curves, DOI: 10.5281/zenodo.4589276), rheologyEvaluation (for analysis of oscillatory sweep rheology, DOI: 10.5281/zenodo.4594353), particleShearEvaluation (evaluation of the output of the Python simulations, DOI: 10.5281/zenodo.4594649), plot.counts (convenience functions for scientific plotting, DOI: 10.5281/zenodo.4589498) and reproducibleCalculationTools (numerical comparision of subsequent evaluations to validate reproducibility, DOI: 10.5281/zenodo.4594515).

For automated evaluation of ImageJ macros from Excel files, we also developed an Excel macro runner plugin in ImageJ, termed PoreSizeExcel (DOI: 10.5281/zenodo.4589546). While the R and Python libraries listed above are actively loaded and used by the CodeOcean capsule, we used the PoreSizeExcel ImageJ plugin manually to streamline our quantitative image treatment, but not in a fully automated fashin.

The Zenodo archives cited above reproducibly provide the state of the libraries as used for evaluation of this dataset, we continue to develop the libraries and continuously make them available at Github ( at https://github.com/tbgitoo ).

Version history

This is the third version of this Zenodo repository.

We undertook major efforts from version v1.0 to the present version v2.0 to increase reprodubility of evaluation (via the use of the CodeOcean platform) and via separation of generic libraries (listed above, and installable on their own independently of this particular project) from specific project-associated data and evaluation (here). For this reason, while the data is maintained and in part completed due to new experiments having been carried out in the mean time, the structure of the repository has undergone major changes from v1.0 to the present version v2.0.

With this version v3.0 we added raw data on cell transplantation, and completed the CodeOcean capsule, including adaptation to peer review changes to the manuscript.