FibroTUG platforms: Time-lapse microscopy dataset of engineered cardiac microbundles

Kobeissi, Hiba1 ; Gao, Xining2; DePalma, Samuel J.3; Ewoldt, Jourdan K.1; Wang, Miranda Chinyun2; Das, Shoshana L.2; Jilberto, Javiera3; Nordsletten, David3; Baker, Brendon M.3; Chen, Christopher S.1; Lejeune, Emma1

Research facility: Boston University, University of Michigan–Ann Arbor*

Published May 03, 2024; Updated May 10, 2024 on Dryad. https://doi.org/10.5061/dryad.3r2280gqd

Abstract

This dataset is a "part II" extension of the "Engineered cardiac microbundle time-lapse microscopy image dataset" and contains 808 experimental time-lapse image sequences of beating hiPSC-based cardiac microbundles using FibroTUG platforms [1] ("Type2"). In the "part I" extension, we include 732 experimental time-lapse image sequences of beating hiPSC-based cardiac microbundles using microbundle strain gauge platforms [2] ("Type1").

References:

[1] DePalma, S. J., Davidson, C. D., Stis, A. E., Helms, A. S., & Baker, B. M. (2021). Microenvironmental determinants of organized iPSC-cardiomyocyte tissues on synthetic fibrous matrices. Biomaterials science, 9(1), 93-107.

[2] Zhang, K., Cloonan, P. E., Sundaram, S., Liu, F., Das, S. L., Ewoldt, J. K., ... & Chen, C. S. (2021). Plakophilin-2 truncating variants impair cardiac contractility by disrupting sarcomere stability and organization. Science Advances, 7(42), eabh3995.

README: FibroTUG platforms: Time-lapse microscopy dataset of engineered cardiac microbundles

https://doi.org/10.5061/dryad.3r2280gqd

This dataset is a "part II" extension of the Engineered cardiac microbundle time-lapse microscopy image dataset and contains 808 experimental time-lapse image sequences of beating hiPSC-based cardiac microbundles using FibroTUG platforms [1] ("Type2"). In "part I" extension, we include 732 experimental time-lapse image sequences of beating hiPSC-based cardiac microbundles using microbundle strain gauge platforms [2] ("Type1").

Description of the data and file structure

We include here 808 examples of "Type 2" tissue. We share the raw videos in ".tif" format and organize them based on: 1) platform type ("Type 2"), 2) experimental conditions under which the microbundles were grown ("condition_000", "condition_001",...), and 3) the batch of differentiated CMs ("batch_000", "batch_001",...) and is reflected in the folder naming. For practical reasons, we made sure that each zipped folder is less than 10GB in size, and as such, some folders were split into multiple ones. For example, "Type2_condition_000_batch_001_00.zip" and "Type2_condition_000_batch_001_01.zip" both correspond to data obtained for microbundles grown with "Type 2" platforms, under "condition 0" conditions, and for CMs from the same batch.

Additionally, we include a metadata file ("metadata_type2.csv") that includes the "file_name", "experimental_conditions", "batch", "comments", and "included_in_plot". While "file_name", "experimental_conditions", and "batch" are straightforward to comprehend, "comments" correspond to remarks regarding running each specific example with MicroBundlePillarTrack software available on GitHub. The "included_in_plot" column is used to indicate if the example was included (marked by "1") or not (marked by "0") in the summary output plot included in the main figure of the accompanying manuscript. We note that the keys for the number coded entries in "experimental_conditions" and "comments" are included in "Type2_experimental_conditions.pdf" and "Comments_key.pdf" files.

Code/Software

We publish this dataset to accompany our pillar tracking software (MicroBundlePillarTrack) published on GitHub. In fact, we have tested our pipeline on all 1540 examples included in this dataset and the Strain gauge platforms: Time-lapse microscopy dataset of engineered cardiac microbundles dataset.

References

Methods

In brief, experimental platforms of "Type 2" consist of electrospun fiber matrices suspended between a pair of PDMS cantilevers fabricated by soft lithography. Differentiated and purified iPSC-CMs were patterned onto the functionalized matrices using microfabricated seeding masks. After 3–21 days of seeding, time-lapse videos of the microbundle’s spontaneous contractions were acquired.

The 808 examples included in this dataset were grown under 21 different tissue culture conditions, as detailed in the "Type2_experimental_conditions.pdf" document. The document "Type2_common_experimental_metadata.pdf" summarizes the common experimental conditions.

Usage notes

As previously mentioned, we include 808 examples of "Type 2" tissue. We share the raw videos in ".tif" format and organize them based on: 1) platform type ("Type 2"), 2) experimental conditions under which the microbundles were grown ("condition_000", "condition_001",...), and 3) the batch of differentiated CMs ("batch_000", "batch_001",...) and is reflected in the folder naming. For practical reasons, we made sure that each zipped folder is less than 10GB in size, and as such, some folders were split into multiple ones. For example, "Type2_condition_000_batch_001_00.zip" and "Type2_condition_000_batch_001_01.zip" both correspond to data obtained for microbundles grown with "Type 2" platforms, under "condition 0" conditions, and for CMs from the same batch.

Additionally, we include a metadata file ("metadata_type2.csv") that includes the "file_name", "experimental_conditions", "batch", "comments", and "included_in_plot". While "file_name", "experimental_conditions", and "batch" are straightforward to comprehend, "comments" correspond to remarks regarding running each specific example with MicroBundlePillarTrack software available on GitHub. The "included_in_plot" column is used to indicate if the example was included (marked by "1") or not (marked by "0") in the summary output plot included in the main figure of the accompanying manuscript. We note that the keys for the number-coded entries in "experimental_conditions" and "comments" are included in the "Type2_experimental_conditions.pdf" and "Comments_key.pdf" files.