Stain Deconvolution Using Statistical Analysis of Multi-Resolution Stain Colour Representation

Alsubaie, Najah; Trahearn, Nicholas; Raza, Shan E. Ahmed; Snead, David; Rajpoot, Nasir M.

doi:10.1371/journal.pone.0169875

Cited by 70 publications

(60 citation statements)

References 22 publications

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“…Regions of interest were captured at x100 magnification using a Leica DM2000LED microscope and LAS software with a pixel resolution of 0.04 μm/pixel. Stain separation of the fast blue, fast red and nonspecific background signals were achieved using a python implementation of the independent component analysis approach 54 . The resulting deconvoluted images were analysed using a custom rule set built in the object-oriented machine learning software Developer XD (Definiens AG, Munich, Germany).…”

Section: Mutz-3 Differentiation and Ev Treatmentmentioning

confidence: 99%

Exosomes transmit retroelement RNAs to drive inflammation and immunosuppression in Ewing Sarcoma

Evdokimova

Ruzanov

Gassmann

et al. 2019

Preprint

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Ewing sarcoma (EwS) is an aggressive childhood malignancy with a high propensity for metastasis. By analyzing cohorts of patients and age-matched healthy donors, we establish that EwS metastatic progression is accompanied by elevated plasma levels of multiple proinflammatory cytokines, interferons and extracellular vesicles (EVs). The latter were enriched with transcripts derived from LINE, SINE and ERV retroelements and from locus-specific pericentromeric regions, including HSAT2. We show that some of these RNAs, including HSAT2 and HERV-K, are selectively transmitted in EwS EVs and taken up by stromal fibroblasts and peripheral blood CD33 + myeloid cells and CD8 + T-cells, inducing immune exhaustion, immunosuppressive phenotypes and proinflammatory responses. Moreover, EwS EV-derived repeat RNAs were propagated and serially transmitted in recipient cell EVs, reminiscent of viral infection. As such, this study uncovers a novel mechanism driving cancer-associated inflammation, immunosuppression and metastatic progression.

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Section: Mutz-3 Differentiation and Ev Treatmentmentioning

confidence: 99%

Exosomes transmit retroelement RNAs to drive inflammation and immunosuppression in Ewing Sarcoma

Evdokimova

Ruzanov

Gassmann

et al. 2019

Preprint

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“…During image analysis, the colour deconvolution (CD) method was employed due to the heterogeneity of lymph node tissue 15,45 . Colour deconvolution allows the separation of RGB colours from images into stain channels made with specific vectors 46,47 . These stain channels are in grayscale and correspond to the intensity of a particular stain found in the image 46 .…”

Section: Discussionmentioning

confidence: 99%

“…Colour deconvolution allows the separation of RGB colours from images into stain channels made with specific vectors 46,47 . These stain channels are in grayscale and correspond to the intensity of a particular stain found in the image 46 . This analysis plugin determines the density of stain in areas where multiples stains are co-localized 41 .…”

Section: Discussionmentioning

confidence: 99%

“…Another potential limitation is the use of CD. Color devolution can have pitfalls in its ability to detect dark areas, where brown pigment can be falsely recognized as dark blue pixels 18,46 , usually when stains like diaminobenzidine (DAB) are used. This was seen in our results where SLNs scored as 0 are detected as a category of 1+ by image analysis (8.87%) since dark tissue is recognized as traces of blue.…”

Section: Discussionmentioning

confidence: 99%

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Validating a semi-quantitative method to assess the degree of methylene blue staining in sentinel lymph nodes

Ram

Oblak

Matuszewska

et al. 2020

Preprint

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Validating a semi-quantitative method for assessment of degree of methylene blue staining in sentinel lymph nodes Abstract Purpose: To develop a digital algorithm and validate a semi-quantitative scoring method for surface methylene blue (MB) staining in whole lymph nodes (LN). Methods: Lymph nodes from canine models undergoing sentinel lymph node (SLN) mapping were prospectively assessed ex vivo and photographed. Two blinded observers evaluated all images and assigned a score based on surface staining (0 -no blue stain, 1 -1-50% stained, 2 -51-100% stained). A standard reference for degree of blue staining was based on signal-tobackground ratios using computer-based imaging software with an output measurement of percentage of staining of the LN. Agreement between observers was assessed using the Kappa coefficient. Results: 124 lymph nodes were included and demonstrated strong agreement (K = 0.8007, p < 0.0001) between results of semi-quantitative scoring and image analysis. Also, strong interobserver and intraobserver agreement was observed for the scoring system (K = 0.8051, p < 0.0001 and K = 0.9493, p < 0.0001, respectively). Discussion: Agreement between scoring system and imaging software illustrates a validated method in assessing MB staining, without the need for analysis software. The use of a semiquantitative scoring system shows promise for a simple, objective assessment of MB staining in surgery and for future study. Lymph nodes can have variable surface colour, which can make assessment of blue staining challenging for novice observers in certain cases. This study describes a digital algorithm for quantitative analysis of blue staining in LN thereby providing a novel and objective reporting mechanism in scientific research involving SLN mapping.

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“…Quite a few [25,72,73,94] have utilized deep learning to perform a multimodal registration. Deep learning is also used for the separation of staining colors [3,3,20,39,93] or for registration [10,27,28].…”

Section: Deep Learningmentioning

confidence: 99%

The tempest in a cubic millimeter: Image-based refinements necessitate the reconstruction of 3D microvasculature from a large series of damaged alternately-stained histological sections

Lobachev

2019

Preprint

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This work presents two methods that facilitate a 3D reconstruction of microscopic blood vessels in the volume slightly larger than 1 mm 3 . The source of the data are histological serial sections, i. e., microscopic images of probes, stained with immunohistochemistry. Odd and even sections have different stainings in our primary data set. Thus, firstly, an approach to register an alternately-stained series is presented. With image filtering and a feature-detection-based registration we obtain a registered stack of 148 serial sections. The series has missing sections, locally damaged sections, artifacts from acquisition. All these hinder correct connectivity of blood vessels. With our second approach we interpolate the missing information while maintaining the connectivity. We achieve this with deformations based on dense optical flow. The presented methodology is applicable to further histological series. A combination of both approaches allows us to reconstruct more than 76 % larger volumes. An important detail was the composition mode of images. Summarizing, we use methods from image processing and computer vision to create large-scale 3D models from immunostained histological serial sections.

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Stain Deconvolution Using Statistical Analysis of Multi-Resolution Stain Colour Representation

Cited by 70 publications

References 22 publications

Exosomes transmit retroelement RNAs to drive inflammation and immunosuppression in Ewing Sarcoma

Exosomes transmit retroelement RNAs to drive inflammation and immunosuppression in Ewing Sarcoma

Validating a semi-quantitative method to assess the degree of methylene blue staining in sentinel lymph nodes

The tempest in a cubic millimeter: Image-based refinements necessitate the reconstruction of 3D microvasculature from a large series of damaged alternately-stained histological sections

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