Kardiopulmonale Reanimation

Gohlke, H.; Gohlke-Bärwolf, Ch.

doi:10.1007/978-3-642-96617-0_35

Cited by 4 publications

(4 citation statements)

References 18 publications

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“…We implemented the algorithm using the Python library, version 3.9. Openslide[24] and tifffile[25] for low-level WSI operations, Numpy[26] for fast numerical computations, Shapely[27] for geometry processing, and OpenCV[28] and Pillow[29] for image processing algorithms.…”

Section: Methodsmentioning

confidence: 99%

PathEX: Make Good Choice for Whole Slide Image Extraction

Yang,

Zhang,

Yang

et al. 2024

Preprint

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BackgroundThe tile-based approach has been widely used for slide-level predictions in whole slide image (WSI) analysis. However, the irregular shapes and variable dimensions of tumor regions pose challenges for the process. To address this issue, we proposed PathEX, a framework that integrates intersection over tile (IoT) and background over tile (BoT) algorithms to extract tile images around boundaries of annotated regions while excluding the blank tile images within these regions.MethodsWe developed PathEX, which incorporated IoT and BoT into tile extraction, for training a classification model in CAM (239 WSIs) and PAIP (40 WSIs) datasets. By adjusting the IoT and BoT parameters, we generated eight training sets and corresponding models for each dataset. The performance of PathEX was assessed on the testing set comprising 13,076 tile images from 48 WSIs of CAM dataset and 6,391 tile images from 10 WSIs of PAIP dataset.ResultsPathEX could extract tile images around boundaries of annotated region differently by adjusting the IoT parameter, while exclusion of blank tile images within annotated regions achieved by setting the BoT parameter. As adjusting IoT from 0.1 to 1.0, and 1 - BoT from 0.0 to 0.5, we got 8 train sets. Experimentation revealed that set C demonstrates potential as the most optimal candidate. Nevertheless, a combination of IoT values ranging from 0.2 to 0.5 and 1-BoT values ranging from 0.2 to 0.5 also yielded favorable outcomes.ConclusionsIn this study, we proposed PathEX, a framework that integrates IoT and BoT algorithms for tile image extraction at the boundaries of annotated regions while excluding blank tiles within these regions. Researchers can conveniently set the thresholds for IoT and BoT to facilitate tile image extraction in their own studies. The insights gained from this research provide valuable guidance for tile image extraction in digital pathology applications.

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Section: Methodsmentioning

confidence: 99%

PathEX: Make Good Choice for Whole Slide Image Extraction

Yang,

Zhang,

Yang

et al. 2024

Preprint

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“…Masks for each cell were acquired by implementing Cellpose 2.0 using the cyto2 model with the parameters 120 in diameter and −0.5 in mask threshold 31 . Tifffile, Pandas, and NumPy were used for image loading, data handling, and numerical operations, respectively 32–34 . Cells in the boundary of the field of view were removed from the extracted intensities.…”

Section: Methodsmentioning

confidence: 99%

Mitochondrial reactive oxygen species modify extracellular vesicles secretion rate

Nørgård,

Lund,

Kalisi

et al. 2023

FASEB BioAdvances

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Extracellular vesicle (EV) secretion rate is stimulated by hypoxia that causes increased reactive oxygen species (ROS) production by the mitochondrial electron transport chain (ETC) and hypoxia‐induced factor (HIF)‐1 signaling; however, their contribution to the increased EV secretion rate is unknown. We found that the EV marker secretion rate in our EV reporter cell line CD9truc‐EGFP was unaffected by the HIF‐1α stabilizer roxadustat; yet, ETC stimulation by dichloroacetic acid (DCA) significantly increased EV secretion. The DCA‐induced EV secretion was blocked by the antioxidant TEMPO and rotenone, an inhibitor of the ETC's Complex I. Under hypoxic conditions, the limited oxygen reduction impedes the ETC's Complex III. To mimic this, we inhibited Complex III with antimycin A, which increased ROS‐dependent EV secretion. The electron transport between Complex I and III is accomplished by coenzyme Q created by the mevalonate pathway and tyrosine metabolites. Blocking an early step in the mevalonate pathway using pitavastatin augmented the DCA‐induced EV secretion, and 4‐nitrobenzoate—an inhibitor of the condensation of the mevalonate pathway with tyrosine metabolites—increased ROS‐dependent EV secretion. Our findings indicate that hypoxia‐mimetics targeting the ETC modify EV secretion and that ROS produced by the ETC is a potent stimulus for EV secretion.

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“…Building on the large number of functions already available in NumPy ( Van der Walt et al, 2011), SciPy (Virtanen et al, 2020), scikit-image (Van der Walt et al, 2014 and making use of tifffile (Gohlke, 2020) and meshio (Schlömer et al, 2020), the spam project adds a large amount of functionality, which means that a number of advanced forms of data analysis can be chained together in ways that are otherwise complex, requiring the combination of many different tools.…”

Section: Technical Detailsmentioning

confidence: 99%