Frauke Wilm, Michaela Benz, Volker Bruns, Serop Baghdadlian, Jakob Dexl, David Hartmann, Petr Kuritcyn, Martin Weidenfeller, Thomas Wittenberg, Susanne Merkel, Arndt Hartmann, Markus Eckstein, Carol Immanuel Geppert
Purpose: Automatic outlining of different tissue types in digitized histological specimen provides a basis for follow-up analyses and can potentially guide subsequent medical decisions. The immense size of whole-slide-images (WSIs), however, poses a challenge in terms of computation time. In this regard, the analysis of nonoverlapping patches outperforms pixelwise segmentation approaches but still leaves room for optimization. Furthermore, the division into patches, regardless of the biological structures they contain, is a drawback due to the loss of local dependencies.
Approach: We propose to subdivide the WSI into coherent regions prior to classification by grouping visually similar adjacent pixels into superpixels. Afterward, only a random subset of patches per superpixel is classified and patch labels are combined into a superpixel label. We propose a metric for identifying superpixels with an uncertain classification and evaluate two medical applications, namely tumor area and invasive margin estimation and tumor composition analysis.
Results: The algorithm has been developed on 159 hand-annotated WSIs of colon resections and its performance is compared with an analysis without prior segmentation. The algorithm shows an average speed-up of 41% and an increase in accuracy from 93.8% to 95.7%. By assigning a rejection label to uncertain superpixels, we further increase the accuracy by 0.4%. While tumor area estimation shows high concordance to the annotated area, the analysis of tumor composition highlights limitations of our approach.
Conclusion: By combining superpixel segmentation and patch classification, we designed a fast and accurate framework for whole-slide cartography that is AI-model agnostic and provides the basis for various medical endpoints.
The analysis and interpretation of histopathological samples and images is an important discipline in the diagnosis of
various diseases, especially cancer. An important factor in prognosis and treatment with the aim of a precision medicine
is the determination of so-called cancer stem cells (CSC) which are known for their resistance to chemotherapeutic
treatment and involvement in tumor recurrence. Using immunohistochemistry with CSC markers like CD13, CD133 and
others is one way to identify CSC. In our work we aim at identifying CSC presence on ubiquitous Hematoxilyn and Eosin
(HE) staining as an inexpensive tool for routine histopathology based on their distinct morphological features.
We present initial results of a new method based on color deconvolution (CD) and convolutional neural networks
(CNN). This method performs favorably (accuracy 0.936) in comparison with a state-of-the-art method based on 1DSIFT
and eigen-analysis feature sets evaluated on the same image database. We also show that accuracy of the CNN is
improved by the CD pre-processing.
Malaria is one of the world’s most common and serious tropical diseases, caused by parasites of the genus plasmodia that
are transmitted by Anopheles mosquitoes. Various parts of Asia and Latin America are affected but highest malaria
incidence is found in Sub-Saharan Africa. Standard diagnosis of malaria comprises microscopic detection of parasites in
stained thick and thin blood films. As the process of slide reading under the microscope is an error-prone and tedious
issue we are developing computer-assisted microscopy systems to support detection and diagnosis of malaria.
In this paper we focus on a deep learning (DL) approach for the detection of plasmodia and the evaluation of the
proposed approach in comparison with two reference approaches. The proposed classification schemes have been
evaluated with more than 180,000 automatically detected and manually classified plasmodia candidate objects from so-called
thick smears. Automated solutions for the morphological analysis of malaria blood films could apply such a
classifier to detect plasmodia in the highly complex image data of thick smears and thereby shortening the examination
time. With such a system diagnosis of malaria infections should become a less tedious, more reliable and reproducible
and thus a more objective process. Better quality assurance, improved documentation and global data availability are
additional benefits.
The morphological analysis of bone marrow smears is fundamental for the diagnosis of leukemia. Currently, the counting and classification of the different types of bone marrow cells is done manually with the use of bright field microscope. This is a time consuming, partly subjective and tedious process. Furthermore, repeated examinations of a slide yield intra- and inter-observer variances. For this reason an automation of morphological bone marrow analysis is pursued. This analysis comprises several steps: image acquisition and smear detection, cell localization and segmentation, feature extraction and cell classification. The automated classification of bone marrow cells is depending on the automated cell segmentation and the choice of adequate features extracted from different parts of the cell. In this work we focus on the evaluation of support vector machines (SVMs) and random forests (RFs) for the differentiation of bone marrow cells in 16 different classes, including immature and abnormal cell classes. Data sets of different segmentation quality are used to test the two approaches. Automated solutions for the morphological analysis for bone marrow smears could use such a classifier to pre-classify bone marrow cells and thereby shortening the examination duration.
Bladder cancer is one of the most common cancers in the western world. The diagnosis in Germany
is based on the visual inspection of the bladder. This inspection performed with a cystoscope is a
challenging task as some kinds of abnormal tissues do not differ much in their appearance from their
surrounding healthy tissue. Fluorescence Cystoscopy has the potential to increase the detection rate.
A liquid marker introduced into the bladder in advance of the inspection is concentrated in areas with
high metabolism. Thus these areas appear as bright "glowing". Unfortunately, the fluorescence image
contains besides the glowing of the suspicious lesions no more further visual information like for example
the appearance of the blood vessels. A visual judgment of the lesion as well as a precise treatment
has to be done using white light illumination. Thereby, the spatial information of the lesion provided
by the fluorescence image has to be guessed by the clinical expert. This leads to a time consuming
procedure due to many switches between the modalities and increases the risk of mistreatment. We
introduce an automatic approach, which detects and segments any suspicious lesion in the fluorescence
image automatically once the image was classified as a fluorescence image. The area of the contour
of the detected lesion is transferred to the corresponding white light image and provide the clinical
expert the spatial information of the lesion. The advantage of this approach is, that the clinical expert
gets the spatial and the visual information of the lesion together in one image. This can save time and
decrease the risk of an incomplete removal of a malign lesion.
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