Omkar2118/datasets huggingface dataset:
Strain gauge platforms: Time-lapse microscopy dataset of engineered cardiac microbundles

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 "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. 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. 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.

Introducing paper: MicroBundlePillarTrack: A Python package for automated segmentation, tracking, and analysis of pillar deflection in cardiac microbundles
FibroTUG platforms: Time-lapse microscopy dataset of engineered cardiac microbundles

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*
[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.

Introducing paper: MicroBundlePillarTrack: A Python package for automated segmentation, tracking, and analysis of pillar deflection in cardiac microbundles