'Cloudbuster': a Python-based open source application for three-dimensional reconstruction and quantification of stacked biological imaging samples.

Three-dimensional (3D) spheroid cultures are generating increasing interest in cancer research, e.g. for the evaluation of pharmacological effects of novel small molecule inhibitors. This is mainly due to the fact that such 3D structures reflect physiological characteristics of tumours and the cellular microenvironments they reside in more faithfully than two-dimensional (2D) cell cultures; in addition, they allow the reduction of animal experiments while providing significantly relevant human-based models. Quantification of such organoid structures as well as the mainly slice-based acquisition and thus forced 2D representation of 3D spheroids provide a challenge for the interpretation of the associated generated data. Here, we provide a novel open-source workflow to reconstruct a 3D entity from slice-recorded microscopical images with or without treatment with anti-migratory small molecule inhibitors. This reconstruction produces distinct point clouds as basis for subsequent comparison of basic readout parameters using average computer processor, memory and graphics resources within an acceptable time frame. We were able to validate the usefulness of this workflow using 3D data generated by various imaging techniques, including z-stacks from confocal microscopy and histochemically labelled spheroid sectioning, and demonstrate the possibility to accurately characterize inhibitor effects in great detail.

Comparison of LI-RADS with other non-invasive liver MRI criteria and radiological opinion for diagnosing hepatocellular carcinoma in cirrhotic livers using gadoxetic acid with histopathological explant correlation.

AIM: To establish the diagnostic accuracy of the Liver Imaging Reporting and Data System (LI-RADS) for hepatocellular carcinoma (HCC) and compare its performance to that of international criteria from European Assofor the Study of the Liver (EASL), Japan Society of Hepatology (JSH), Asian Pacific Association for the Study of the Liver (APASL), and Organ Procurement and Transplantation Network (OPTN), and to the reporting radiologist's overall opinion regarding the probability of a nodule being a HCC by correlating with a histological diagnosis from whole liver explants. MATERIALS AND METHODS: The present single-centre, retrospective review selected participants based on the following criteria: adults (≥18 years) listed for liver transplantation in 2014/2015, with liver cirrhosis at the time of magnetic resonance imaging (MRI) with hepatocyte specific contrast agent, and at least one liver lesion ≥10 mm on MRI with histology from subsequent liver explant for comparison. Each lesion was assessed against international criteria and given a "radiologist opinion" score of 1-5 (1 = definitely benign, 5 = definitely HCC). RESULTS: Total 268 patient records were reviewed, with 105 eligible lesions identified from 47 patients. Median lesion size was 15.5 mm (range 10-68 mm). Sensitivity (%), specificity (%), and positive predictive value (PPV; %) for LI-RADS LR5 was 45, 89, and 89, for LI-RADS LR4+5 + TIV was 61, 80, and 86, for EASL was 44, 86 and 86, for JSH/APASL was 64, 81, and 87, for OPTN was 36, 90, and 88, and for "radiologist impression" of probably or definitely HCC was 79, 79, and 88 respectively. CONCLUSIONS: MRI has moderate sensitivity and good specificity for the diagnosis of HCC with considerable variation depending on criteria used. OPTN criteria have the best specificity, but low sensitivity. "Radiologist opinion" gives highest overall accuracy with increases in sensitivity and reduction in specificity when compared to the imaging criteria.

The evolution of caste-biasing symbionts in the social hymenoptera.

The separation of individuals into reproductive and worker castes is the defining feature of insect societies. However, caste determination is itself a complex phenomenon, dependent on interacting genetic and environmental factors. It has been suggested by some authors that widespread maternally transmitted symbionts such as Wolbachia may be selected to interfere with caste determination, whilst others have discounted this possibility on theoretical grounds. We argue that there are in fact three distinct evolutionary scenarios in which maternally transmitted symbionts might be selected to influence the process of caste determination in a social hymenopteran host. Each of these scenarios generate testable predictions which we outline here. Given the increasing recognition of the complexity and multi-faceted nature of caste determination in social insects, we argue that maternally transmitted symbionts should also be considered as possible factors influencing the development of social hymenopterans.

Digital cytology: A short review of technical and methodological approaches and applications.

The recent years have been characterised by a rapid development of whole slide imaging (WSI) especially in its applications to histology. The application of WSI technology to cytology is less common because of technological problems related to the three-dimensional nature of cytology preparations (which requires capturing of z-stack information, with an increase in file size and usability issues in viewing cytological preparations). The aim of this study is to provide a review of the literature on the use of digital cytology and provide an overview of cytological applications of WSI in current practice as well as identifying areas for future development.

Three-dimensional digital reconstruction of human placental villus architecture in normal and complicated pregnancies.

OBJECTIVE: This study aimed to examine the use of digital technology in the three-dimensional reconstruction of human placentas. STUDY DESIGN: Placentas obtained at term elective caesarean section were sampled, formalin-fixed and embedded in paraffin. Two hundred 5 µm consecutive sections were cut from each specimen and the resultant slides stained with haematoxylin and eosin. Slides were then scanned and the digitised images reconstructed using customised software. RESULTS: Three-dimensional reconstructions were successfully achieved in placentas from normal pregnancies and those complicated by pre-eclampsia, growth restriction, and gestational diabetes. Marked morphological differences were readily identifiable, most clearly in the stem villus architecture. CONCLUSION: This method is an emerging research tool for examining placental histoarchitecture at high resolution and gaining clinically relevant insight into the placental pathology allied to pregnancy complications such as PET, IUGR and GD.

The anatomy of the perineal body in relation to abdominoperineal excision for low rectal cancer.

AIM: Dissection of the perineal body (PB) during abdominoperineal excision (APE) for low rectal cancer is often difficult due to the lack of a natural plane of dissection. Understanding the PB and its relation to the anorectum is essential to permit safe dissection during the perineal phase of the operation and avoid damage to the anorectum and urogenital organs. This study describes the anatomy and histology of the PB relevant to APE. METHOD: Six human adult cadaver pelvic exenteration specimens (three male, three female) from the Leeds GIFT Research Tissue Programme were studied. Paraffin-embedded mega-blocks were produced and serially sectioned at 50- and 250-µm intervals. Sections were stained by immunohistochemistry to show collagen, elastin and smooth muscle. RESULTS: The PB was cylindrically shaped in the male specimens and wedge-shaped in the female ones. Although centrally located between the anal and urogenital triangles, it was nearly completely formed by muscle fibres derived from the rectal muscularis propria. Thick bundles of smooth muscle, mostly arising from the longitudinal muscle, inserted into the PB and levator ani muscle (LAM). The recto-urethralis muscle originated from the PB and separated the anterolateral PB from the urogenital organs. CONCLUSION: Smooth muscle fibres derived from the rectal muscularis propria extend into the PB and LAM and appear to fix the anorectum. Dissection of the PB during APE is safe only when the smooth muscle fibres that extend into the PB are divided.

Understanding the surgical pitfalls in total mesorectal excision: Investigating the histology of the perirectal fascia and the pelvic autonomic nerves.

AIM: Excellent understanding of fasciae and nerves surrounding the rectum is necessary for total mesorectal excision (TME). However, fasciae anterolateral to the rectum and surrounding the low rectum are still poorly understood. We studied the perirectal fascia enfolding the extraperitoneally located part of the rectum in en-bloc cadaveric specimens and the University Medical Center Utrecht (UMCU) pelvic dataset, and describe implications for TME. METHODS: Four donated human adult cadaveric specimens (two males, two females) were obtained through the Leeds GIFT Research Tissue Programme. Paraffin-embedded blocks were produced and serially sectioned at 50 and 250 µm intervals. Whole mount sections were stained with haematoxylin & eosin, Masson's trichrome and Millers' elastin. Additionally, the UMCU pelvic dataset including digitalised cryosections of a female pelvis in three axes was studied. RESULTS: The mid and lower rectum were surrounded by a multi-layered perirectal fascia, of which the mesorectal fascia (MRF) and parietal fascia bordered the 'holy plane'. There was no extra constant fascia forming a potential surgical plane. Nerves ran laterally to the MRF. More caudally, the mesorectal fat strongly reduced and the MRF approached the rectal muscularis propria. The MRF had a variable appearance in terms of thickness and completeness, most prominently at the anterolateral lower rectum. CONCLUSION: Dissection onto the MRF allows nerve preservation in TME. Rectal surgeons are challenged in doing so as the MRF varies in thickness and shows gaps, most prominently at the anterolateral lower rectum. At this site, the risk of entering the mesorectum is great and may result in an incomplete specimen.

Whole mount microscopic sections reveal that Denonvilliers' fascia is one entity and adherent to the mesorectal fascia; implications for the anterior plane in total mesorectal excision?

BACKGROUND: Excellent anatomical knowledge of the rectum and surrounding structures is essential for total mesorectal excision (TME). Denonviliers' fascia (DVF) has been frequently studied, though the optimal anterior plane in TME is still disputed. The relationship of the lateral edges of DVF to the autonomic nerves and mesorectal fascia is unclear. We studied whole mout microscopic sections of en-bloc cadaveric pelvic exenteration and describe implications for TME. METHODS: Four donated human adult cadaveric specimens (two males, two females) were obtained from the Leeds GIFT Research Tissue Programme. Paraffin-embedded mega blocks were produced and serially sectioned at 50 and 250 µm intervals. Sections were stained with haematoxylin & eosin, Masson's trichrome and Millers' elastin. Additionally, a series of eleven human fetal specimens (embryonic age of 9-20 weeks) were studied. RESULTS: DVF consisted of multiple fascial condensations of collagen and smooth muscle fibres and was indistinguishable from the anterior mesorectal fascia and the prostatic fascia or posterior vaginal wall. The lateral edges of DVF appeared fan-shaped and the most posterior part was continuous with the mesorectal fascia. Fasciae were not identified in fetal specimens. CONCLUSION: DVF is adherent to and continuous with the mesorectal fascia. Optimal surgical dissection during TME should be carried out anterior to DVF to ensure radical removal, particularly for anterior tumours. Autonomic nerves are at risk, but can be preserved by closely following the mesorectal fascia along the anterolateral mesorectum. The lack of evident fasciae in fetal specimens suggested that these might be formed in later developmental stages.

Unsupervised content classification based nonrigid registration of differently stained histology images.

Registration of histopathology images of consecutive tissue sections stained with different histochemical or immunohistochemical stains is an important step in a number of application areas, such as the investigation of the pathology of a disease, validation of MRI sequences against tissue images, multiscale physical modeling, etc. In each case, information from each stain needs to be spatially aligned and combined to ascertain physical or functional properties of the tissue. However, in addition to the gigabyte-size images and nonrigid distortions present in the tissue, a major challenge for registering differently stained histology image pairs is the dissimilar structural appearance due to different stains highlighting different substances in tissues. In this paper, we address this challenge by developing an unsupervised content classification method that generates multichannel probability images from a roughly aligned image pair. Each channel corresponds to one automatically identified content class. The probability images enhance the structural similarity between image pairs. By integrating the classification method into a multiresolution-block-matching-based nonrigid registration scheme (N. Roberts, D. Magee, Y. Song, K. Brabazon, M. Shires, D. Crellin, N. Orsi, P. Quirke, and D. Treanor, "Toward routine use of 3D histopathology as a research tool," Amer. J. Pathology, vol. 180, no. 5, 2012.), we improve the performance of registering multistained histology images. Evaluation was conducted on 77 histological image pairs taken from three liver specimens and one intervertebral disc specimen. In total, six types of histochemical stains were tested. We evaluated our method against the same registration method implemented without applying the classification algorithm (intensity-based registration) and the state-of-the-art mutual information based registration. Superior results are obtained with the proposed method.

The proportion of tumour cells is an independent predictor for survival in colorectal cancer patients.

BACKGROUND: The proportion of epithelial and stromal cells in tumours is thought to have an important role in the progression of epithelial malignancy. We aimed to determine whether the relative proportion of tumour (PoT) was related to survival in colorectal cancer. METHODS: The PoT at the luminal surface was measured by point counting using virtual tissue sections in a series of 145 colorectal cancer cases. The relationship of PoT to clinicopathological parameters including cancer-specific survival was analysed. Modified receiver operating characteristic curves were used to determine the optimum cut off points to dichotomise the data for survival analyses. RESULTS: Tumours with PoT-low (

Pathology of colorectal cancer.

Colorectal cancer is an excellent example of a cancer where outcome can be, and has been, improved by the co-operation of clinicians and pathologists. This article summarises the basics of the pathology of colorectal cancer, with an emphasis on practical issues in clinical practice. The histopathology of colorectal cancer, staging and genetics are discussed, as are more recent developments such as the pathology of neoadjuvant therapy and colorectal cancer screening, and molecular prognostic and predictive factors in colorectal cancer.

Low-grade dysplasia in Barrett's esophagus has a high risk of progression.

BACKGROUND AND STUDY AIMS: Surveillance in Barrett's esophagus relies on the detection of dysplasia by histopathology. However, the natural history of this condition, particularly that of low-grade dysplasia (LGD) is poorly understood. This paper describes our experience of LGD over a period of 21 years. PATIENTS AND METHODS: Between 1984 and January 1995, 357 patients with Barrett's esophagus without dysplasia were recruited for annual surveillance: 34 of these patients developed LGD during this period. This was a retrospective cohort study of this group in terms of survival and cancer outcomes >/= 8 years after the original diagnosis of LGD, comparing them with the patients who did not develop LGD over the same period, with a histopathological review of the original diagnoses of LGD. The outcomes of 356/357 (99.7 %) of the patients were established in December 2004. RESULTS: After 8 years, high-grade dysplasia (HGD) or cancer had developed in 9/34 patients with LGD (27 %) and in 16/322 controls (5 %). Cox's proportional hazards model revealed that the time from the first diagnosis of Barrett's esophagus to the first "event" of either HGD, esophageal cancer, or death did not show a statistically significant difference between the two groups. A further analysis treating death as "loss to follow-up" showed a significantly increased risk for the LGD group to progress to HGD or cancer (hazard ratio 5.9 [95 % confidence interval 2.6 - 13.4], P< 0.001). The histopathology review demonstrated a fair level of agreement between pathologists, with a kappa value of 0.48. CONCLUSIONS: Patients diagnosed with LGD during surveillance of Barrett's esophagus are at a considerably increased risk of progressing to develop esophageal cancer over an 8-year period but most deaths are not cancer-related.

Pathological response following long-course neoadjuvant chemoradiotherapy for locally advanced rectal cancer.

AIMS: To standardize the pathological analysis of total mesorectal excision specimens of rectal cancer following neoadjuvant chemoradiotherapy for locally advanced disease (T3/T4), including tumour regression. METHODS AND RESULTS: Standardized dissection and reporting was used for 60 patients who underwent total mesorectal excision following long-course chemoradiotherapy. Tumour regression was scored by two pathologists (K.S., D.G.) using both an established 5-point tumour regression grade (TRG), and a novel 3-point grade. Both scores were evaluated for interobserver variability. A complete or near-complete pathological response (3-point TRG 1) was found in 10 patients (17%). Using the 5-point TRG, there was good agreement between both pathologists (kappa = 0.64). Using the 3-point grade, agreement was excellent (kappa = 0.84). No disease recurrence has been reported in patients with a complete, or near complete pathological response (3-point TRG 1), after a mean follow-up of 22 months. CONCLUSION: Tumour regression grade is a useful method of scoring tumour response to chemoradiotherapy in rectal cancer. TRG 1 and 2 can be regarded as a complete pathological response (ypT0). A modified 3-point grade has the advantage of better reproducibility, with similar prognostic significance.

Incidence of cervical dyskaryosis in Ireland: report of a five-year audit.

The implementation of a national cervical screening programme in Ireland will require agreement on achievable standards in reporting cervical cytology similar to those published by the NHS cervical screening programme. Due to the opportunistic nature of screening in the Republic of Ireland, national incidence figures for uterine cervical disease are not available. An audit of our practice was performed to find the incidence of human papilloma virus related cervical disease in our population. Our laboratory reported 158,066 cases from 1996-2000. The overall rate of dyskaryosis increased from 3.6% to 7.9%, mostly due to increased low grade dyskaryosis (up from 2.3% to 6.0%). High grade dyskaryosis also increased (from 1.3% to 1.9%), particularly in the under-25 year age group who account for a growing proportion of high grade dyskaryosis (from 15.4% of all high grade diagnoses in 1996 to 23.0% in 2000). The positive predictive value of a diagnosis of high grade dyskaryosis remained stable between 76.0 and 79.5%. While opportunistic screening data may not be directly applicable to the entire screening population it is hoped that these data may form a foundation on which to estimate national incidence figures and define achievable standards for cervical screening cytology in Ireland.