DOI: 10.5281/zenodo.10838384
title: Histological Dataset for Microvascular Segmentation of Tissue-Engineered Vascular Grafts

description: Objectives: The pursuit of understanding vascular tissue regeneration within tissue-engineered vascular grafts (TEVGs) is of paramount importance due to the critical role these grafts play in replacing damaged or diseased blood vessels. TEVGs offer a promising alternative to traditional grafts, with the potential to integrate into the host's tissue and support the natural regenerative processes. However, challenges such as thrombosis, inflammation, and the need for grafts that can adapt to the dynamic biological environment remain. By studying the regenerative processes in TEVGs, researchers can gain insights into the mechanisms that underpin successful graft integration and function, which is essential for improving patient outcomes in vascular surgeries. This dataset, with its detailed annotations of histological features, provides a valuable resource for developing and refining machine-learning models that can analyze and predict patterns of vascular tissue regeneration. The ability to accurately segment and quantify microvessels and immune cells in regenerated arteries is a significant step forward in distinguishing between physiological and pathological regeneration, ultimately contributing to the design of more effective and reliable TEVGs for clinical use.

Ethical Approval: Experimental strategy of the study is described in detail in [1] and [2]. The study was conducted according to the guidelines of the Declaration of Helsinki, and was approved by the Local Ethical Committee of the Research Institute for Complex Issues of Cardiovascular Diseases (Kemerovo, Russia, protocol code 2020/06, date of approval: 19 February 2020). Animal experiments were performed in accordance with the European Convention for the Protection of Vertebrate Animals (Strasbourg, 1986) and Directive 2010/63/EU of the European Parliament on the protection of animals used for scientific purposes. For the implantation, we used female Edilbay sheep of 42–45 kg body weight which were received from the Animal Core Facility of the Research Institute for Complex Issues of Cardiovascular Diseases (Kemerovo, Russia) and selected for the surgery by Doppler ultrasonography to identify those having carotid artery diameter of 4.0 ± 0.2 mm.

Description: The dataset comprises a collection of Whole Slide Images (WSIs) obtained from biodegradable TEVGs implanted into the carotid arteries of 20 sheep. A total of 104 WSIs were acquired, each measuring an average size of 135,000 x 123,000 pixels. These WSIs were stained using Hematoxylin and Eosin (H&E), a common practice for highlighting the structure of tissue sections, which facilitates the detailed examination of histological features. These WSIs were automatically sliced into 99,831 patches of 3,000 x 3,000 pixels and subsequently filtered, resulting in 1,401 selected patches for manual annotation.

Annotation Method: Two pathologists independently selected and meticulously annotated the 1401 patches, identifying nine distinct histological features associated with vascular tissue regeneration. These features include arteriole lumen (AL), arteriole media (AM), arteriole adventitia (AA), venule lumen (VL), venule wall (VW), capillary lumen (CL), capillary wall (CW), immune cells (IC), and nerve trunks (NT). The annotations were performed using binary masks, delineating each feature within the patches. Subsequently, a senior pathologist conducted a triple verification process, reviewing and refining the annotations to ensure accuracy and consistency. The annotations are provided in the form of binary masks, meticulously defined for each feature within the patches.

Dataset Split: Given the limited number of subjects studied, comprising 20 sheep, we employed a 5-fold cross-validation technique to split our dataset. This method was chosen because it allows for the efficient use of limited data, ensuring that each observation has the opportunity to be used in both the training and testing sets, thus reducing bias and providing a more accurate estimate of the model's performance. In this approach, each fold involved 16 sheep for training and the remaining 4 for testing (see Table 1 and Figure 3). This partitioning scheme was consistently applied to maintain the integrity of subject groups within each subset and to prevent data leakage. The 5-fold cross-validation is particularly beneficial for our study's objectives as it maximizes the training data available for developing robust machine learning models while also ensuring that the models are tested on unseen data, thereby enhancing the generalizability of our findings.

Access to the Study: Further information about this study, including curated source code, dataset details, and trained models, can be accessed through the following repositories:



Source code: https://github.com/ViacheslavDanilov/histology_segmentation

Dataset: https://doi.org/10.5281/zenodo.10838384

Models: https://doi.org/10.5281/zenodo.10838431


 

Table 1. Patch and feature distributions across folds and subsets






Fold



Subset



Patches



AL



AM



AA



VL



VW



CL



CW



IC



NT



Total 





1



Train



1168



510



512



220



675



648



770



765



409



448



4957



1


Test



233



81



84



36



186



169



178



182



91



25



1032





2



Train



1053



406



411



179



678



638



743



746



423



315



4539



2


Test



348



185



185



77



183



179



205



201



77



158



1450





3



Train



1127



507



511



222



743



702



759



760



299



423



4926



3


Test



274



84



85



34



118



115



189



187



201



50



1063





4



Train



1064



466



472



199



611



566



759



758



423



291



4545



4


Test



337



125



124



57



250



251



189



189



77



182



1444





5



Train



1192



475



478



204



737



714



761



759



446



415



4989



5


Test



209



116



118



52



124



103



187



188



54



58



1000