DOI: 10.5061/dryad.3r2280gqd
title: FibroTUG platforms: Time-lapse microscopy dataset of engineered cardiac microbundles

description: 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.
description: 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. 
description: # FibroTUG platforms: Time-lapse microscopy dataset of engineered cardiac
 microbundles
 [https://doi.org/10.5061/dryad.3r2280gqd](https://doi.org/10.5061/dryad.3r2280gqd) This dataset is a "part II" extension of the [`Engineered cardiac microbundle time-lapse microscopy image dataset`](https://doi.org/10.5061/dryad.5x69p8d8g) 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](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 "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](https://github.com/HibaKob/MicroBundlePillarTrack). 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 \[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.