Deep Learning-based Framework for Automatic Cranial Defect Reconstruction and Implant Modeling

The goal of this work is to propose a robust, fast, and fully automatic method for personalized cranial defect reconstruction and implant modeling. We propose a two-step deep learning-based method using a modified U-Net architecture to perform the defect reconstruction, and a dedicated iterative procedure to improve the implant geometry, followed by automatic generation of models ready for 3-D printing. We propose a cross-case augmentation based on imperfect image registration combining cases from different datasets. We perform ablation studies regarding different augmentation strategies and compare them to other state-of-the-art methods. We evaluate the method on three datasets introduced during the AutoImplant 2021 challenge, organized jointly with the MICCAI conference. We perform the quantitative evaluation using the Dice and boundary Dice coefficients, and the Hausdorff distance. The average Dice coefficient, boundary Dice coefficient, and the 95th percentile of Hausdorff distance are 0.91, 0.94, and 1.53 mm respectively. We perform an additional qualitative evaluation by 3-D printing and visualization in mixed reality to confirm the implant's usefulness. We propose a complete pipeline that enables one to create the cranial implant model ready for 3-D printing. The described method is a greatly extended version of the method that scored 1st place in all AutoImplant 2021 challenge tasks. We freely release the source code, that together with the open datasets, makes the results fully reproducible. The automatic reconstruction of cranial defects may enable manufacturing personalized implants in a significantly shorter time, possibly allowing one to perform the 3-D printing process directly during a given intervention. Moreover, we show the usability of the defect reconstruction in mixed reality that may further reduce the surgery time.

Automatic Nonrigid Histological Image Registration with Adaptive Multistep Algorithm

In this paper, we present a short description of the method proposed to ANHIR challenge organized jointly with the IEEE ISBI 2019 conference. We propose a method consisting of preprocessing, initial alignment, nonrigid registration algorithms and a method to automatically choose the best result. The method turned out to be robust (99.792% robustness) and accurate (0.38% average median rTRE). The main drawback of the proposed method is relatively high computation time. However, this aspect can be easily improved by cleaning the code and proposing a GPU implementation.