CAIMAN: An online algorithm repository for Cancer Image Analysis

Reyes-Aldasoro, Constantino Carlos; Griffiths, Michael K.; Savas, Deniz; Tozer, Gillian M.

doi:10.1016/j.cmpb.2010.07.007

Cited by 15 publications

(12 citation statements)

References 13 publications

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“…The cells were imaged immediately and at intervals for up to 24 h with a Nikon Eclipse phase contrast microscope equipped with a Digital Slight DS camera and NIS-Elements software. Wound closure was quantified with an automatic image analysis algorithm [23] using the CAIMAN image analysis website (http://www.caiman.org.uk/). …”

Section: Methodsmentioning

confidence: 99%

Tumour Cells Expressing Single VEGF Isoforms Display Distinct Growth, Survival and Migration Characteristics

et al. 2014

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Vascular endothelial growth factor-A (VEGF) is produced by most cancer cells as multiple isoforms, which display distinct biological activities. VEGF plays an undisputed role in tumour growth, vascularisation and metastasis; nevertheless the functions of individual isoforms in these processes remain poorly understood. We investigated the effects of three main murine isoforms (VEGF188, 164 and 120) on tumour cell behaviour, using a panel of fibrosarcoma cells we developed that express them individually under endogenous promoter control. Fibrosarcomas expressing only VEGF188 (fs188) or wild type controls (fswt) were typically mesenchymal, formed ruffles and displayed strong matrix-binding activity. VEGF164- and VEGF120-producing cells (fs164 and fs120 respectively) were less typically mesenchymal, lacked ruffles but formed abundant cell-cell contacts. On 3D collagen, fs188 cells remained mesenchymal while fs164 and fs120 cells adopted rounded/amoeboid and a mix of rounded and elongated morphologies respectively. Consistent with their mesenchymal characteristics, fs188 cells migrated significantly faster than fs164 or fs120 cells on 2D surfaces while contractility inhibitors accelerated fs164 and fs120 cell migration. VEGF164/VEGF120 expression correlated with faster proliferation rates and lower levels of spontaneous apoptosis than VEGF188 expression. Nevertheless, VEGF188 was associated with constitutively active/phosphorylated AKT, ERK1/2 and Stat3 proteins. Differences in proliferation rates and apoptosis could be explained by defective signalling downstream of pAKT to FOXO and GSK3 in fs188 and fswt cells, which also correlated with p27/p21 cyclin-dependent kinase inhibitor over-expression. All cells expressed tyrosine kinase VEGF receptors, but these were not active/activatable suggesting that inherent differences between the cell lines are governed by endogenous VEGF isoform expression through complex interactions that are independent of tyrosine kinase receptor activation. VEGF isoforms are emerging as potential biomarkers for anti-VEGF therapies. Our results reveal novel roles of individual isoforms associated with cancer growth and metastasis and highlight the importance of understanding their diverse actions.

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Section: Methodsmentioning

confidence: 99%

Tumour Cells Expressing Single VEGF Isoforms Display Distinct Growth, Survival and Migration Characteristics

et al. 2014

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“…CAIMAN is an Image Analysis internet‐based project (Reyes‐Aldasoro et al, 2010) that combines the scripting language PHP (The PHP group, free software), the high‐level technical computing language MATLAB (The Mathworks), the Interactive Object Management Environment (IOME) Markup Language (Griffiths et al, 2009) and specifically designed image analysis algorithms ((Reyes‐Aldasoro et al, 2008; Reyes‐Aldasoro, 2009) for instance), to provide a user‐friendly web‐page where any person can upload images from their experiments and execute analysis algorithms to obtain quantitative measurements. The website and the use of IOME have been presented in more detail in (Griffiths et al, 2009; Reyes‐Aldasoro et al, 2010), but in brief: the user selects the appropriate algorithm from those available through the CAIMAN website and uploads the image to be analysed. Once the images have been uploaded to the web‐server, the IOME‐PHP toolbox is used to make a web service request to the image analysis service, which resides in a high performance cluster, this request is made using IOME‐ML.…”

Section: Resultsmentioning

confidence: 99%

An automatic algorithm for the segmentation and morphological analysis of microvessels in immunostained histological tumour sections

Reyes-Aldasoro

Williams

Akerman

et al. 2010

Journal of Microscopy

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SummaryA fully automatic segmentation and morphological analysis algorithm for the analysis of microvessels from CD31 immunostained histological tumour sections is presented. Development of the algorithm exploited the distinctive hues of stained vascular endothelial cells, cell nuclei and background, to provide the seeds for a 'region-growing' method for object segmentation in the 3D hue, saturation, value (HSV) colour model. The segmented objects, identified as microvessels by CD31 immunostaining, were post-processed with three morphological tasks: joining separate objects that were likely to belong to a single vessel, closing objects that had a narrow gap around their periphery, and splitting objects with multiple lumina into individual vessels. The automatic segmentation was validated against a hand-segmented set of 44 images from three different SW1222 human colorectal carcinomas xenografted into mice. 96.3 ± 0.9% of pixels were found to be correctly classified. Automated segmentation was carried out on a further 53 images from three histologically distinct mouse fibrosarcomas (MFs) for morphological comparison with the SW1222 tumours. Four morphometric measurements were calculated for each segmented vessel: vascular area (VA), ratio of lumen area to vascular area (lu/VA), eccentricity (e), and roundness (ro). In addition, the total vascular area relative to tumour tissue area (rVA) was calculated. lu/VA, e and ro were found to be significantly smaller in MF tumours than in SW1222 tumours (p < 0.05; unpaired t-test). The algorithm is available through the website http://www.caiman.org.uk where images can be uploaded, processed and sent back to users. The output from CAIMAN consists of the original image with boundaries of segmented vessels overlaid, the Correspondence to:

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“…Based on constructed binary images (threshold between 210 and 220 RGB values of intensity) the percentage of hypoxia positive stained area in tumor slides was determined. MVD and average vessel area was determined using online image segmentation and endothelial cell analysis software CAIMAN (CAncer IMage ANalysis: http://www.caiman.org.uk ) [ 18 ] in 5 selected ROIs. ROIs, excluding necrotic regions and artifacts, were manually drawn to represent entire slide (pixel size 0.088 × 0.088 μm).…”

Section: Methodsmentioning

confidence: 99%

The use of matrigel has no influence on tumor development or PET imaging in FaDu human head and neck cancer xenografts

et al. 2016

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BackgroundIn preclinical research MatrixgelTM Basement Membrane Matrix (MG) is used frequently for the establishment of syngeneic and xenograft cancer models. Limited information on its influence on parameters including; tumor growth, vascularization, hypoxia and imaging characteristics is currently available. This study evaluates the potential effect of matrigel use in a human head and neck cancer xenograft model (FaDu; hypopharyngeal carcinoma) in NMRI nude mice. The FaDu cell line was chosen based on its frequent use in studies of cancer imaging and tumor microenvironment.MethodsNMRI nude mice (n = 34) were divided into two groups and subcutaneously injected with FaDu cells in medium either including (+MG) or excluding matrigel (−MG). In sub study I seven mice from each group (+MG, n = 7; −MG, n = 7) were 18F- fluorodeoxyglucose (18F-FDG) PET/CT scanned on Day 5, 8, 12, 15, and 19. In sub study II ten mice from each group (+MG, n = 10; −MG, n = 10) were included and tumors collected for immunohistochemistry (IHC) analysis of tumor microenvironment including; proliferation ratio, micro vessel density, average vessel area, hypoxia, nuclear density, and necrosis. Tumors for IHC were collected according to size (200–400 mm3, 500–700 mm3, 800–1100 mm3).ResultsFDG uptake and tumor growth was statistically compatible for the tumors established with or without MG. The IHC analysis on all parameters only identified a significantly higher micro vessel density for tumor size 500–700 mm3 and 800–1100 mm3 and average vessel area for tumor size 500–700 mm3 in the −MG group. Comparable variations were observed for tumors of both the +MG and −MG groups. No difference in tumor take rate was observed between groups in study.ConclusionsMatrigel did not affect tumor growth or tumor take for the FaDu xenograft model evaluated. Tumors in the -MG group displayed increased angiogenesis compared to the +MG tumors. No difference in 18F-FDG PET uptake for tumors of different groups was found. Based on these observations the influence of matrigel on tumor imaging and tumor microenvironment seems minor for this particular xenograft model.

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CAIMAN: An online algorithm repository for Cancer Image Analysis

Abstract: This is the unspecified version of the paper.This version of the publication may differ from the final published version. Permanent repository link

Cited by 15 publications

References 13 publications

Tumour Cells Expressing Single VEGF Isoforms Display Distinct Growth, Survival and Migration Characteristics

Tumour Cells Expressing Single VEGF Isoforms Display Distinct Growth, Survival and Migration Characteristics

An automatic algorithm for the segmentation and morphological analysis of microvessels in immunostained histological tumour sections

The use of matrigel has no influence on tumor development or PET imaging in FaDu human head and neck cancer xenografts

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