Engineered Cardiac Microbundle Time-Lapse Microscopy Image Dataset

The "Microbundle Time-lapse Dataset" contains 24 experimental time-lapse images of cardiac microbundles using three distinct types of experimental testbed of beating lab grown hiPSC-based cardiac microbundles. 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].

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.  

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).

[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, under review (2023).

Introducing paper: MicroBundleCompute: Automated segmentation, tracking, and analysis of subdomain deformation in cardiac microbundles