Multimodal Lung Cancer Subtyping Using Deep Learning Neural Networks on Whole Slide Tissue Images and MALDI MSI.

Artificial intelligence (AI) has shown potential for facilitating the detection and classification of tumors. In patients with non-small cell lung cancer, distinguishing between the most common subtypes, adenocarcinoma (ADC) and squamous cell carcinoma (SqCC), is crucial for the development of an effective treatment plan. This task, however, may still present challenges in clinical routine.

Robust subtyping of non-small cell lung cancer whole sections through MALDI mass spectrometry imaging.

Subtyping of the most common non-small cell lung cancer (NSCLC) tumor types adenocarcinoma (ADC) and squamous cell carcinoma (SqCC) is still a challenge in the clinical routine and a correct diagnosis is crucial for an adequate therapy selection. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) has shown potential for NSCLC subtyping but is subject to strong technical variability and has only been applied to tissue samples assembled in tissue microarrays (TMAs). To our knowledge, a successful transfer of a classifier from TMAs to whole sections, which are generated in the standard clinical routine, has not been presented in the literature as of yet.

Deeply Supervised UNet for Semantic Segmentation to Assist Dermatopathological Assessment of Basal Cell Carcinoma.

Accurate and fast assessment of resection margins is an essential part of a dermatopathologist's clinical routine. In this work, we successfully develop a deep learning method to assist the dermatopathologists by marking critical regions that have a high probability of exhibiting pathological features in whole slide images (WSI). We focus on detecting basal cell carcinoma (BCC) through semantic segmentation using several models based on the UNet architecture.

Cross-Normalization of MALDI Mass Spectrometry Imaging Data Improves Site-to-Site Reproducibility.

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is an established tool for the investigation of formalin-fixed paraffin-embedded (FFPE) tissue samples and shows a high potential for applications in clinical research and histopathological tissue classification. However, the applicability of this method to serial clinical and pharmacological studies is often hampered by inevitable technical variation and limited reproducibility. We present a novel spectral cross-normalization algorithm that differs from the existing normalization methods in two aspects: (a) it is based on estimating the full statistical distribution of spectral intensities and (b) it involves applying a non-linear, mass-dependent intensity transformation to align this distribution with a reference distribution.

Using the Chemical Noise Background in MALDI Mass Spectrometry Imaging for Mass Alignment and Calibration.

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is an established tool for the investigation of formalin fixed paraffin embedded (FFPE) tissue samples and shows a high potential for applications in clinical research and histopathological diagnosis. The applicability and accuracy of this method, however, heavily depends on the quality of the acquired data, and in particular mass misalignment in axial time-of-flight (TOF) MSI continues to be a serious issue. We present a mass alignment and recalibration method that is specifically designed to operate on MALDI peptide imaging data.