DOI: 10.5061/dryad.sqv9s4nbg
title: Strain gauge platforms: Time-lapse microscopy dataset of engineered cardiac microbundles

description: This dataset is a "part I" extension of the "Engineered
 cardiac microbundle time-lapse microscopy image dataset" and contains
 732 experimental time-lapse image sequences of beating hiPSC-based cardiac
 microbundles using microbundle strain gauge platforms [1]
 ("Type1"). In the "part II" extension, we included 808
 experimental time-lapse image sequences of beating hiPSC-based cardiac
 microbundles using FibroTUG platforms [2] ("Type2"). 
 References: [1] 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.
 [2] 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.
description: In brief, standard devices of “Type 1” consist of 2 pillars of
 either circular or rectangular cross-sections with spherical caps. The
 devices were cast from poly(dimethylsiloxane) (PDMS) 3D printed molds and
 were then chemically treated to promote both cell attachment to the pillar
 caps and growth of the microbundle between the two pillars. Following
 sterilization of the device, hiPSC-CMs, differentiated and purified, were
 seeded with human ventricular cardiac fibroblasts and fibrin extracellular
 matrix (ECM) solution. Finally, time-lapse videos of tissue contractions,
 whether beating spontaneously or electrically stimulated with 30V at a 1Hz
 frequency, were taken 5–15 days after seeding. The 732
 examples included in this dataset were grown under 31 different tissue
 culture conditions, as detailed in the
 "Type1_experimental_conditions.pdf" document. The document
 "Type1_common_experimental_metadata.pdf" summarizes the common
 experimental conditions. Usage notes
 As previously mentioned, we include here 732 examples of
 "Type 1" tissue. We share the raw videos in ".tif"
 format and organize them based on: 1) platform type ("Type 1"),
 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. Additionally, we include a metadata file
 ("metadata_type1.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 "Type1_experimental_conditions.pdf" and "Comments_key.pdf" files. 
description: # Strain gauge platforms: Time-lapse microscopy dataset of engineered
 cardiac microbundles
 [https://doi.org/10.5061/dryad.sqv9s4nbg](https://doi.org/10.5061/dryad.sqv9s4nbg) This dataset is a "part I" extension of the "[Engineered cardiac microbundle time-lapse microscopy image dataset](https://doi.org/10.5061/dryad.5x69p8d8g)" and contains 732 experimental time-lapse image sequences of beating hiPSC-based cardiac microbundles using microbundle strain gauge platforms `[1]` ("Type1"). In "part II" extension, we include 808 experimental time-lapse image sequences of beating hiPSC-based cardiac microbundles using FibroTUG platforms `[2]` ("Type2").  ## Description of the data and file structure We include here 732 examples of "Type 1" tissue. We share the raw videos in ".tif" format and organize them based on: `1)` platform type ("Type 1"), `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. Additionally, we include a metadata file ("metadata_type1.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](https://github.com/HibaKob/MicroBundlePillarTrack). 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 "Type1_experimental_conditions.pdf" and "Comments_key.pdf" files.  ## Code/Software We publish this dataset to accompany our pillar tracking software (MicroBundlePillarTrack) published on [GitHub](https://github.com/HibaKob/MicroBundlePillarTrack). In fact, we have tested our pipeline on all 1540 examples included in this dataset and the `FibroTUG platforms: Time-lapse microscopy dataset of engineered cardiac microbundles` dataset. ## References \[1] 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. \[2] 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.