A parallel solution for high resolution histological image analysis

Bueno, Gloria; González, R.; Déniz, Óscar; García-Rojo, Marcial; González-García, J.; Fernández-Carrobles, M. Milagro; Vállez, Noelia; Jesus, S. M.

doi:10.1016/j.cmpb.2012.03.007

Cited by 18 publications

(14 citation statements)

References 29 publications

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“…HE stained prostate biopsies have three types of well-differentiated structures of interest: lumen, cytoplasm, and cells. For pathological purposes, the most important structures are cells [1]. Their morphology, distribution between them, and relationship with lumen and cytoplasm are the most relevant features that pathologists consider to elaborate a diagnosis.…”

Section: Methodsmentioning

confidence: 99%

“…Most of them are focused on the segmentation of only one ROI, usually the nucleus and glands, as well as the extraction of descriptors for classification purposes. A thorough review of the research related to classification may be found in Bueno et al [1]. Statistical information techniques, region growing algorithms [2], fuzzy c-means [3] active contour models, including level set methods [4,5], filtering and morphological analysis [2,5,6] have been also used for ROI detection.…”

Section: Introductionmentioning

confidence: 99%

“…Moreover, level set methods have not been used in a general way, only applied to one type of histological images HE biopsies). In a recent work by the authors [1], a general solution is described for parallelizing in an efficient way a set of heterogeneous low and high-level image processing algorithms to be applied to high resolution histopathological WSI. The imaging tools implemented in [1] are general for all types of histological images with different stain, acquired from different anatomical parts and digitized at different magnifications.…”

Section: Introductionmentioning

confidence: 99%

“…In a recent work by the authors [1], a general solution is described for parallelizing in an efficient way a set of heterogeneous low and high-level image processing algorithms to be applied to high resolution histopathological WSI. The imaging tools implemented in [1] are general for all types of histological images with different stain, acquired from different anatomical parts and digitized at different magnifications. These tools deal with contrast analysis, ROI detection and classification applied to high resolution images that range from 300 MB to 30 GB.…”

Section: Introductionmentioning

confidence: 99%

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An entropy-based automated approach to prostate biopsy ROI segmentation

et al. 2013

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

An entropy-based automated approach to prostate biopsy ROI segmentation

et al. 2013

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“…Unfortunately, segmentation of such images is not an easy task. Most computer-based procedures for immunohistochemistry image analysis [4]- [7] have limited applicability due to numerous drawbacks.…”

Section: Introductionmentioning

confidence: 99%

Short survey: adaptive threshold methods used to segment immunonegative cells from simulated images of follicular lymphoma stained with 3,3'-Diaminobenzidine&Haematoxylin

Roszkowiak

Korzyńska

Pijanowska

2015

Annals of Computer Science and Information Systems

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Abstract-We perform a short survey of image thresholding methods for very specific task, and assess their performance comparison. We analyse performance of adaptive thresholding methods concerning segmentation of immunonegative cells of follicular lymphoma tissue samples stained with 3,3'-Diaminobenzidine&Haematoxylin. We use artificial images based on experimental images that greatly simulates real samples and simplifies process of evaluation. We chose 8 methods of adaptive threshold segmentation, with different approach. They were applied to 6 different monochromatic images derived from original RGB images, by splitting layers, conversion to Lab colour space and colour deconvolution. Evaluation of the results was performed with basic statistical measures as sensitivity and specificity along with Jaccard's coefficient. We identify the thresholding algorithms with superior performance. Collected results will be used to design the new better method based on this approach.

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An automated system for whole microscopic image acquisition and analysis

Bueno

Déniz

Fernández-Carrobles

et al. 2014

Microsc. Res. Tech.

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The field of anatomic pathology has experienced major changes over the last decade. Virtual microscopy (VM) systems have allowed experts in pathology and other biomedical areas to work in a safer and more collaborative way. VMs are automated systems capable of digitizing microscopic samples that were traditionally examined one by one. The possibility of having digital copies reduces the risk of damaging original samples, and also makes it easier to distribute copies among other pathologists. This article describes the development of an automated high-resolution whole slide imaging (WSI) system tailored to the needs and problems encountered in digital imaging for pathology, from hardware control to the full digitization of samples. The system has been built with an additional digital monochromatic camera together with the color camera by default and LED transmitted illumination (RGB). Monochrome cameras are the preferred method of acquisition for fluorescence microscopy. The system is able to digitize correctly and form large high resolution microscope images for both brightfield and fluorescence. The quality of the digital images has been quantified using three metrics based on sharpness, contrast and focus. It has been proved on 150 tissue samples of brain autopsies, prostate biopsies and lung cytologies, at five magnifications: 2.5×, 10×, 20×, 40×, and 63×. The article is focused on the hardware set-up and the acquisition software, although results of the implemented image processing techniques included in the software and applied to the different tissue samples are also presented.

show abstract

A parallel solution for high resolution histological image analysis

Cited by 18 publications

References 29 publications

An entropy-based automated approach to prostate biopsy ROI segmentation

An entropy-based automated approach to prostate biopsy ROI segmentation

Short survey: adaptive threshold methods used to segment immunonegative cells from simulated images of follicular lymphoma stained with 3,3'-Diaminobenzidine&Haematoxylin

An automated system for whole microscopic image acquisition and analysis

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