DOI: 10.5061/dryad.5x69p8d8g
title: Engineered cardiac microbundle time-lapse microscopy image dataset

description: The "Microbundle Time-lapse Dataset" contains 24 experimental
 time-lapse images of cardiac microbundles using three distinct types of
 experimental testbeds. Of the 24 experimental time-lapse images, 23
 examples are brightfield videos, and a single example is a phase contrast
 video. We categorize the different experimental testbeds into 3 types,
 where "Type 1" includes movies obtained from standard
 experimental microbundle platforms termed microbundle strain gauges
 [1,2,3]. We refer to data collected from non-standard platforms termed
 FibroTUGs [4] as "Type 2" data, and "Type 3" data
 represents a highly versatile and diverse nanofabricated experimental
 platform [5,6]. References: [1] Boudou T, Legant WR, Mu A, Borochin MA,
 Thavandiran N, Radisic M, Zandstra PW, Epstein JA, Margulies KB, Chen CS.
 A microfabricated platform to measure and manipulate the mechanics of
 engineered cardiac microtissues. Tissue Engineering Part A. 2012 May
 1;18(9-10):910-9. [2] Xu F, Zhao R, Liu AS, Metz T, Shi Y, Bose P, Reich
 DH. A microfabricated magnetic actuation device for mechanical
 conditioning of arrays of 3D microtissues. Lab on a Chip.
 2015;15(11):2496-503. [3] Bielawski KS, Leonard A, Bhandari S, Murry CE,
 Sniadecki NJ. Real-time force and frequency analysis of engineered human
 heart tissue derived from induced pluripotent stem cells using magnetic
 sensing. Tissue Engineering Part C: Methods. 2016 Oct 1;22(10):932-40. [4]
 DePalma SJ, Davidson CD, Stis AE, Helms AS, Baker BM. Microenvironmental
 determinants of organized iPSC-cardiomyocyte tissues on synthetic fibrous
 matrices. Biomaterials science. 2021;9(1):93-107. [5] Jayne RK, Karakan
 MÇ, Zhang K, Pierce N, Michas C, Bishop DJ, Chen CS, Ekinci KL, White AE.
 Direct laser writing for cardiac tissue engineering: a microfluidic heart
 on a chip with integrated transducers. Lab on a Chip. 2021;21(9):1724-37.
 [6] Karakan MÇ. A Direct-Laser-Written Heart-on-a-Chip Platform for
 Generation and Stimulation of Engineered Heart Tissues (Doctoral
 dissertation, Boston University, 2023).
description: We include here a brief description of the 3
 data types. For "Type 1" testbeds, each experimental tissue well
 consisted of 2 pillars with rectangular cross sections and spherical caps
 cast from poly(dimethylsiloxane) (PDMS) using a 3D printed mold. Following
 treatment to promote cell attachment to the spherical caps, hiPSC-CMs,
 differentiated and purified, were seeded with human ventricular cardiac
 fibroblasts. And after 5-7 days of seeding, time-lapse videos of tissue
 contractions were acquired.  As for
 "Type 2" experimental platforms, arrays of PDMS cantilevers were
 fabricated by soft lithography. Then, fiber matrices were generated by
 selective photo-crosslinking of electrospun dextran vinyl sulfone (DVS)
 fibers and suspended between pairs of cantilevers. After functionalizing
 the electrospun fiber matrices, iPSC-CMs, differentiated and purified,
 were patterned onto matrices using microfabricated seeding masks cast from
 3D-printed molds. Finally, time-lapse videos of the microtissue’s
 spontaneous contractions were taken after 7 days of seeding. 
 Finally, seeding platforms from "Type
 3" were generated using a combination of soft lithography and
 two-photon direct laser writing (DLW). Briefly, the process involves
 printing negative master molds using DLW, casting PDMS onto the molds,
 followed by sandwiching, curing and demolding. Then, cage-like
 micron-scale structures were printed using DLW on the sides of the wells
 of the demolded PDMS devices to facilitate cell attachment. Differentiated
 and purified hiPSC-CMs were seeded into the wells and time-lapse videos of
 the tissue contractions were obtained 4-9 days after seeding. Of note,
 these platforms allow for mechanical actuation of the microbundle, and
 within this dataset, we include "Example_01" which is subjected
 to sawtooth actuation.  We note
 that more details about testbed fabrication, tissue preparation protocols,
 and imaging procedures for each type of the 3 experimental platforms are
 included in the accompanying file "Microbundle_metadata.pdf" and
 its machine-readable version in ".csv" format. We note that
 cells containing "N/A" indicate that the details provided for
 the other tissue engineering platform types are not applicable to this
 specific type.
description: Within this dataset, we include 11 examples
 of "Type 1" tissue, 7 examples of "Type 2" tissue, and
 6 examples of "Type 3" tissue, totaling to 24 different examples
 of these experimental data. In addition to the raw videos shared in
 ".tif" format, we include the tissue masks, whether generated
 automatically via our computational pipeline [7] or manually via tracing
 in ImageJ [8], that were used to run the "MicroBundleCompute"
 software [7] for analyzing these data. These masks are included within the
 "masks" subfolders, where each mask text file is a
 two-dimensional array in which the tissue domain is denoted by “1” and the
 background domain is denoted by “0”. We include the "mask.tif"
 files for visualization purposes only. In brief, this dataset was used to showcase the
 functionality of the "MicroBundleCompute" analysis software [7]
 including pillar tracking and analysis of heterogeneous displacement and
 strain fields. To reproduce the results shown in [9], the manuscript
 introducing the "MicroBundleCompute" software, only a single
 pre-processing step is required. Specifically, the single ".tif"
 file for each experiment needs to be converted into a series of individual
 images saved in the ".TIF" format in the "movie"
 folder.  The code [7] to reproduce all results on this data is available
 in the GitHub repository associated with this manuscript [9] (https://github.com/hibakob/MicroBundleCompute).  <strong>References:</strong> [7] Kobeissi H, & Lejeune E (2023). MicroBundleCompute [Computer software]. https://github.com/HibaKob/MicroBundleCompute [8] Bourne R. Fundamentals of digital imaging in medicine. Springer Science & Business Media; 2010 Jan 18.  [9] Kobeissi H, Jilberto, J, Karakan MÇ, Gao X, DePalma SJ, Das SL, Quach L, Urquia J, Baker BM, Chen CS, Nordsletten D, Lejeune E. MicroBundleCompute: Automated segmentation, tracking, and analysis of sub-domain deformation in cardiac microbundles, in preparation (2023).
description: # Microbundle Time-lapse Dataset --- Brief summary of dataset contents,
 contextualized in experimental procedures and results. ## Abstract The
 "Microbundle Time-lapse Dataset" contains $24$ experimental
 time-lapse images of cardiac microbundles using three distinct types of
 experimental testbeds. Of the $24$ experimental time-lapse images, $23$
 examples are brightfield videos, and a single example is a phase contrast
 video. We categorize the different experimental testbeds into $3$ types,
 where "Type 1" includes movies obtained from standard
 experimental microbundle platforms termed microbundle strain gauges
 [1,2,3]. We refer to data collected from non-standard platforms termed
 FibroTUGs [4] as "Type 2" data, and "Type 3" data
 represents a highly versatile and diverse nanofabricated experimental
 platform [5,6]. ## Methods: We include here a brief description of the 3
 data types. For "Type 1" testbeds, each experimental tissue well
 consisted of $2$ pillars with rectangular cross sections and spherical
 caps cast from poly(dimethylsiloxane) (PDMS) using a 3D printed mold.
 Following treatment to promote cell attachment to the spherical caps,
 hiPSC-CMs, differentiated and purified, were seeded with human ventricular
 cardiac fibroblasts. And after $5-7$ days of seeding, time-lapse videos of
 tissue contractions were acquired. As for "Type 2" experimental
 platforms, arrays of PDMS cantilevers were fabricated by soft lithography.
 Then, fiber matrices were generated by selective photo-crosslinking of
 electrospun dextran vinyl sulfone (DVS) fibers and suspended between pairs
 of cantilevers. After functionalizing the electrospun fiber matrices,
 iPSC-CMs, differentiated and purified, were patterned onto matrices using
 microfabricated seeding masks cast from 3D-printed molds. Finally,
 time-lapse videos of the microtissues spontaneous contractions were taken
 after $7$ days of seeding. Finally, seeding platforms from "Type
 3" were generated using a combination of soft lithography and
 two-photon direct laser writing (DLW). Briefly, the process involves
 printing negative master molds using DLW, casting PDMS onto the molds,
 followed by sandwiching, curing and demolding. Then, cage-like
 micron-scale structures were printed using DLW on the sides of the wells
 of the demolded PDMS devices to facilitate cell attachment. Differentiated
 and purified hiPSC-CMs were seeded into the wells and time-lapse videos of
 the tissue contractions were obtained $4-9$ days after seeding. Of note,
 these platforms allow for mechanical actuation of the microbundle, and
 within this dataset, we include "Example_01" which is subjected
 to sawtooth actuation. We note that more details about testbed
 fabrication, tissue preparation protocols, and imaging procedures for each
 type of the 3 experimental platforms are included in the accompanying file
 "Microbundle_metadata.pdf" and its machine-readable version in
 ".csv" format. We note that cells containing "N/A"
 indicate that the details provided for the other tissue engineering
 platform types are not applicable to this specific type. ## Usage notes:
 Within this dataset, we include 11 examples of "Type 1" tissue,
 7 examples of "Type 2" tissue, and 6 examples of "Type
 3" tissue, totaling to 24 different examples of these experimental
 data. In addition to the raw videos shared in ".tif" format, we
 include the tissue masks, whether generated automatically via our
 computational pipeline [7] or manually via tracing in ImageJ [8], that
 were used to run the "MicroBundleCompute" software [7] for
 analyzing these data. These masks are included within the
 "masks" subfolders, where each mask text fileis a
 two-dimensional array in which the tissue domain is denoted by 1 and the
 background domain is denoted by 0. We include the "mask.tif"
 files for visualization purposes only. In brief, this dataset was used to
 showcase the functionality of the "MicroBundleCompute" analysis
 software [7] including pillar tracking and analysis of heterogeneous
 displacement and strain fields. To reproduce the results shown in [9], the
 manuscript introducing the "MicroBundleCompute" software, only a
 single pre-processing step is required. Specifically, the single
 ".tif" file for each experiment needs to be converted into a
 series of individual images saved in the ".TIF" format in the
 "movie" folder. The code [7] to reproduce all results on this
 data is available in the GitHub repository associated with this manuscript
 [9]
 ([https://github.com/hibakob/MicroBundleCompute](https://github.com/hibakob/MicroBundleCompute)). ### References: \[1] Boudou T, Legant WR, Mu A, Borochin MA, Thavandiran N, Radisic M, Zandstra PW, Epstein JA, Margulies KB, Chen CS. A microfabricated platform to measure and manipulate the mechanics of engineered cardiac microtissues. Tissue Engineering Part A. 2012 May 1;18(9-10):910-9. \[2] Xu F, Zhao R, Liu AS, Metz T, Shi Y, Bose P, Reich DH. A microfabricated magnetic actuation device for mechanical conditioning of arrays of 3D microtissues. Lab on a Chip. 2015;15(11):2496-503. \[3] Bielawski KS, Leonard A, Bhandari S, Murry CE, Sniadecki NJ. Real-time force and frequency analysis of engineered human heart tissue derived from induced pluripotent stem cells using magnetic sensing. Tissue Engineering Part C: Methods. 2016 Oct 1;22(10):932-40. \[4] DePalma SJ, Davidson CD, Stis AE, Helms AS, Baker BM. Microenvironmental determinants of organized iPSC-cardiomyocyte tissues on synthetic fibrous matrices. Biomaterials science. 2021;9(1):93-107. \[5] Jayne RK, Karakan M, Zhang K, Pierce N, Michas C, Bishop DJ, Chen CS, Ekinci KL, White AE. Direct laser writing for cardiac tissue engineering: a microfluidic heart on a chip with integrated transducers. Lab on a Chip. 2021;21(9):1724-37. \[6] Karakan M. A Direct-Laser-Written Heart-on-a-Chip Platform for Generation and Stimulation of Engineered Heart Tissues (Doctoral dissertation, Boston University, 2023). \[7] Kobeissi H, & Lejeune E (2023). MicroBundleCompute [Computer software]. [https://github.com/HibaKob/MicroBundleCompute](https://github.com/HibaKob/MicroBundleCompute) \[8] Bourne R. Fundamentals of digital imaging in medicine. Springer Science & Business Media; 2010 Jan 18. \[9] Kobeissi H, Jilberto, J, Karakan M, Gao X, DePalma SJ, Das SL, Quach L, Urquia J, Baker BM, Chen CS, Nordsletten D, Lejeune E. MicroBundleCompute: Automated segmentation, tracking, and analysis of sub-domain deformation in cardiac microbundles, in preparation (2023). ## Related work MicroBundleCompute: [https://github.com/HibaKob/MicroBundleCompute](https://github.com/HibaKob/MicroBundleCompute)