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Register a new userCytology Image Analysis Techniques Towards Automation: Systematically Revisited
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Cytology is the branch of pathology which deals with the microscopic examination of cells for diagnosis of carcinoma or inflammatory conditions. Automation in cytology started in the early 1950s with the aim to reduce manual efforts in diagnosis of cancer. The inflush of intelligent technological units with high computational power and improved specimen collection techniques helped to achieve its technological heights. In the present survey, we focus on such image processing techniques which put steps forward towards the automation of cytology. We take a short tour to 17 types of cytology and explore various segmentation and/or classification techniques which evolved during last three decades boosting the concept of automation in cytology. It is observed, that most of the works are aligned towards three types of cytology: Cervical, Breast and Lung, which are discussed elaborately in this paper. The user-end systems developed during that period are summarized to comprehend the overall growth in the respective domains. To be precise, we discuss the diversity of the state-of-the-art methodologies, their challenges to provide prolific and competent future research directions inbringing the cytology-based commercial systems into the mainstream.
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The goals of this dissertation are to fully automate the image processing techniques needed in the post-operative stage of IGCIP and to perform a thorough analysis of (a) the robustness of the automatic image processing techniques used in IGCIP and (b) assess the sensitivity of the IGCIP process as a whole to individual components. The automatic methods that have been developed include the automatic localization of both closely- and distantly-spaced CI electrode arrays in post-implantation CTs and the automatic selection of electrode configurations based on the stimulation patterns. Together with the existing automatic techniques developed for IGCIP, the proposed automatic methods enable an end-to-end IGCIP process that takes pre- and post-implantation CT images as input and produces a patient-customized electrode configuration as output.
Lossy image compression has been studied extensively in the context of typical loss functions such as RMSE, MS-SSIM, etc. However, compression at low bitrates generally produces unsatisfying results. Furthermore, the availability of massive public image datasets appears to have hardly been exploited in image compression. Here, we present a paradigm for eliciting human image reconstruction in order to perform lossy image compression. In this paradigm, one human describes images to a second human, whose task is to reconstruct the target image using publicly available images and text instructions. The resulting reconstructions are then evaluated by human raters on the Amazon Mechanical Turk platform and compared to reconstructions obtained using state-of-the-art compressor WebP. Our results suggest that prioritizing semantic visual elements may be key to achieving significant improvements in image compression, and that our paradigm can be used to develop a more human-centric loss function. The images, results and additional data are available at https://compression.stanford.edu/human-compression
We report an object tracking algorithm that combines geometrical constraints, thresholding, and motion detection for tracking of the descending aorta and the network of major arteries that branch from the aorta including the iliac and femoral arteries. Using our automated identification and analysis, arterial system was identified with more than 85% success when compared to human annotation. Furthermore, the reported automated system is capable of producing a stenosis profile, and a calcification score similar to the Agatston score. The use of stenosis and calcification profiles will lead to the development of better-informed diagnostic and prognostic tools.
With the rise of deep learning, there has been increased interest in using neural networks for histopathology image analysis, a field that investigates the properties of biopsy or resected specimens traditionally manually examined under a microscope by pathologists. However, challenges such as limited data, costly annotation, and processing high-resolution and variable-size images make it difficult to quickly iterate over model designs. Throughout scientific history, many significant research directions have leveraged small-scale experimental setups as petri dishes to efficiently evaluate exploratory ideas. In this paper, we introduce a minimalist histopathology image analysis dataset (MHIST), an analogous petri dish for histopathology image analysis. MHIST is a binary classification dataset of 3,152 fixed-size images of colorectal polyps, each with a gold-standard label determined by the majority vote of seven board-certified gastrointestinal pathologists and annotator agreement level. MHIST occupies less than 400 MB of disk space, and a ResNet-18 baseline can be trained to convergence on MHIST in just 6 minutes using 3.5 GB of memory on a NVIDIA RTX 3090. As example use cases, we use MHIST to study natural questions such as how dataset size, network depth, transfer learning, and high-disagreement examples affect model performance. By introducing MHIST, we hope to not only help facilitate the work of current histopathology imaging researchers, but also make the field more-accessible to the general community. Our dataset is available at https://bmirds.github.io/MHIST.
Medical images such as 3D computerized tomography (CT) scans and pathology images, have hundreds of millions or billions of voxels/pixels. It is infeasible to train CNN models directly on such high resolution images, because neural activations of a single image do not fit in the memory of a single GPU/TPU, and naive data and model parallelism approaches do not work. Existing image analysis approaches alleviate this problem by cropping or down-sampling input images, which leads to complicated implementation and sub-optimal performance due to information loss. In this paper, we implement spatial partitioning, which internally distributes the input and output of convolutional layers across GPUs/TPUs. Our implementation is based on the Mesh-TensorFlow framework and the computation distribution is transparent to end users. With this technique, we train a 3D Unet on up to 512 by 512 by 512 resolution data. To the best of our knowledge, this is the first work for handling such high resolution images end-to-end.
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