Histological Artifacts Research Articles

A MORPHOLOGICAL AND BIOLOGICAL ASSESSMENT OF CRENOBIA ALPINA AND CRENOBIA MONTENIGRINA IN PARÂNG-CARPATHIAN MOUNTAINS (ROMANIA), (PLATYHELMINTHES, TRICLADIDA, PLANARIIDAE)

The paper analyses the morphology of the copulatory apparatus and the reproductive isolation of the monopharyngeal and polypharyngeal Crenobia (Dana, 1766) in sympatric populations in Parâng Mt., Romania. The copulatory apparatus of the two forms shows a non-simultaneous development, indicating a seasonal reproductive isolation: the monopharyngeal alpina becomes able to mate during the warm season while the polypharyngeal montenigrina becomes able to mate during the cold season. The mature copulatory apparatus of the monopharyngeals and the polypharyngeals shows all the characters typical for Crenobia alpina (Dana, 1766), respectively for Crenobia montenigrina (Mrázek, 1904) as presented in the literature. In both species, some specimens reveal a complex system of fine ducts / sclerotized lines into the wall of the genital atrium, which are attributed to biological structures of unknown function rather than histological artefacts.

Are you sure it’s an artifact? Artifact detection and uncertainty quantification in histological images

Modern cancer diagnostics involves extracting tissue specimens from suspicious areas and conducting histotechnical procedures to prepare a digitized glass slide, called Whole Slide Image (WSI), for further examination. These procedures frequently introduce different types of artifacts in the obtained WSI, and histological artifacts might influence Computational Pathology (CPATH) systems further down to a diagnostic pipeline if not excluded or handled. Deep Convolutional Neural Networks (DCNNs) have achieved promising results for the detection of some WSI artifacts, however, they do not incorporate uncertainty in their predictions. This paper proposes an uncertainty-aware Deep Kernel Learning (DKL) model to detect blurry areas and folded tissues, two types of artifacts that can appear in WSIs. The proposed probabilistic model combines a CNN feature extractor and a sparse Gaussian Processes (GPs) classifier, which improves the performance of current state-of-the-art artifact detection DCNNs and provides uncertainty estimates. We achieved 0.996 and 0.938 F1 scores for blur and folded tissue detection on unseen data, respectively. In extensive experiments, we validated the DKL model on unseen data from external independent cohorts with different staining and tissue types, where it outperformed DCNNs. Interestingly, the DKL model is more confident in the correct predictions and less in the wrong ones. The proposed DKL model can be integrated into the preprocessing pipeline of CPATH systems to provide reliable predictions and possibly serve as a quality control tool.

Postmortem histological freeze-thaw artifacts: a case report of a frozen infant and literature review.

Freezing and thawing have the potential to alter the gross and histologic appearance of tissues, causing damage to individual cells and disrupting the overall architecture. In forensic investigations, freezing and thawing can play a crucial role in cases of unknown cause of death. Perpetrators may use freezing preservation to conceal the body or obscure the time of death. Freezing can also occur naturally when a body is exposed to the elements, sometimes even leading to death itself. We present a case report involving an autopsy performed on an infant, who died of natural causes, after undergoing freezing and thawing. The objective of this study was to identify and discuss the histological artifacts observed in different tissues as a result of the freeze-thaw process. Histologically, the infant's tissues exhibited the most common features described in the literature. Ice crystal artifacts, characterized by expansion of the extracellular space and tissue clefts, were found in the heart, brain, liver, lungs, and kidneys. On the contrary, adipose tissue was not affected, likely due to the scarcity of water. Freeze-thaw artifacts should be taken into account whether a body is known to have been frozen or to add further data if found already defrosted.

Histological artifacts associated with laser and electroscalpel gingivectomy: Case series

Introduction. Over time, efforts have been invested in the design of new instruments that overcome the disadvantages of the gold standard instrument in surgery, the scalpel. As a result, electronic equipment has emerged such as the electric scalpel and laser devices. The available evidence on these instruments suggests that the tissue response is related to each instrument’s physical and biological cutting principles. Objective. To compare the histological changes in gingiva samples associated with surgical cutting performed with a 940 nm diode laser, a 2780 nm erbium, chromium: yttriumscandium-gallium-garnet (Er,Cr:YSGG) laser, and an electric scalpel, by presenting a series of cases. Case presentation. We present three cases of healthy patients undergoing cosmetic surgery. The clinical examination revealed exposure of a keratinized gingiva band greater than 4 mm, normal color and texture in gingival tissue, with a firm consistency and no bleeding on periodontal probing. Gingivectomy was indicated with the following protocols: Diode laser of 940 nm at 1 W, in continuous mode; Er,Cr:YSGG laser of 2780 nm at 2.5 W, 75 Hz, H mode, air 20, water 40, gold tip MT4); and electric scalpel in cutting mode at power level four. Gingival tissue samples were taken and stored in 10% formaldehyde for histological analysis. Conclusion. All the evaluated cutting instruments generated histological changes produced by the thermal effect, the main ones being collagen coagulation and carbonization. The depth of thermal damage caused by the 2780 nm Er,Cr:YSGG laser was much lesser than that induced by the electric scalpel and the 940 nm diode laser.

Formalin-free fixation and xylene-free tissue processing preserves cell-hydrogel interactions for histological evaluation of 3D calcium alginate tissue engineered constructs

Histological evaluation of tissue-engineered products, including hydrogels for cellular encapsulation, is a critical and invaluable tool for assessing the product across multiple stages of its lifecycle from manufacture to implantation. However, many tissue-engineered products are comprised of polymers and hydrogels which are not optimized for use with conventional methods of tissue fixation and histological processing. Routine histology utilizes a combination of chemical fixatives, such as formaldehyde, and solvents such as xylene which have been optimized for use with native biological tissues due to their high protein and lipid content. Previous work has highlighted the challenges associated with processing hydrogels for routine histology due to their high water content and lack of diverse chemical moieties amenable for tissue fixation with traditional fixatives. Thus, hydrogel-based tissue engineering products are prone to histological artifacts during their validation which can lead to challenges in correctly interpreting results. In addition, chemicals used in conventional histological approaches are associated with significant health and environmental concerns due to their toxicity and there is thus an urgent need to identify suitable replacements. Here we use a multifactorial design of experiments approach to identify processing parameters capable of preserving cell-biomaterial interactions in a prototypical hydrogel system: ionically crosslinked calcium alginate. We identify a formalin free fixative which better retains cell-biomaterial interactions and calcium alginate hydrogel integrity as compared to the state-of-the-art formalin-based approaches. In addition, we demonstrate that this approach is compatible with a diversity of manufacturing techniques used to fabricate calcium alginate-based scaffolds for tissue engineering and cell therapy, including histological evaluation of cellular encapsulation in 3D tubes and thin tissue engineering scaffolds (∼50 μm). Furthermore, we show that formalin-free fixation can be used to retain cell-biomaterial interactions and hydrogel architecture in hybrid alginate-gelatin based scaffolds for use with histology and scanning electron microscopy. Taken together, these findings are a significant step forward towards improving histological evaluation of ionically crosslinked calcium alginate hydrogels and help make their validation less toxic, thus more environmentally friendly and sustainable.

A deep-learning model for transforming the style of tissue images from cryosectioned to formalin-fixed and paraffin-embedded.

Histological artefacts in cryosectioned tissue can hinder rapid diagnostic assessments during surgery. Formalin-fixed and paraffin-embedded (FFPE) tissue provides higher quality slides, but the process for obtaining them is laborious (typically lasting 12-48 h) and hence unsuitable for intra-operative use. Here we report the development and performance of a deep-learning model that improves the quality of cryosectioned whole-slide images by transforming them into the style of whole-slide FFPE tissue within minutes. The model consists of a generative adversarial network incorporating an attention mechanism that rectifies cryosection artefacts and a self-regularization constraint between the cryosectioned and FFPE images for the preservation of clinically relevant features. Transformed FFPE-style images of gliomas and of non-small-cell lung cancers from a dataset independent from that used to train the model improved the rates of accurate tumour subtyping by pathologists.

Artifacts and main lesions in fetal ocular histology

Histological artifacts in fetal eyes can involve different tissues and can be related to mechanical or autolytic lesions, fixation, the cause of death or the cutting technique. Knowing the causes, effects and appearance of artifacts allow the minimization of the risk of avoidable artifacts and help distinguish them from "true" pathological lesions. We describe these different types of artifacts and specifically analyze their involvement in different tissue structures of the eye. We compare them with primary fetal ocular lesions. Given the wide variety of artifacts, the identification of lesions in fetal eyes must be done with caution, since differentiating true lesions from artifacts requires some experience and relies on both macroscopic examination and microscopic analyses, with ideally comparisons with references' images of normal tissues of the same gestational age.

Laparoscopic twist technique has the best overall artifact profile when comparing three laparoscopic hepatic cup biopsy techniques for dogs.

To determine the difference in histologic artifacts and morphologic diagnosis among 3 laparoscopic cup biopsy forceps techniques and wedge hepatic samples. Cadavers of 20 client-owned dogs following euthanasia for unrelated reasons between January 3 and July 29, 2021. Four biopsy techniques were performed from the margin of 3 liver lobes/dog. Laparoscopic techniques used 5-mm cup biopsy forceps to obtain biopsy samples by pulling the forceps forcefully caudally to free a sample (the PULL technique), rotating the forceps 360° in 1 direction until freed (the TWST technique), or pulling the forceps through a 5-mm cannula to remove the sample (the CAN technique); wedge biopsy samples served as the control (CON). Data collected included sample weight, histologic features, diagnosis, and artifact characterization. Gwet AC1 or intraclass correlation coefficients (ICCs) were calculated to detect agreement among techniques. Sample weights for CON and TWST were significantly larger (P < .001 and P = .035, respectively) than for PULL and CAN. There was excellent agreement among all techniques for most diagnostic features (Gwet AC1, 0.93 to 1). The TWST technique resulted in the best overall artifact profile for laparoscopic techniques, with 90% of samples (54/60) having crisp edges and 65% of samples (39/60) having no or mild tearing. The agreement was moderate to good (ICC, 0.73 for edges and 0.76 for tearing) among all cup biopsy forceps techniques. The TWST technique resulted in the largest sample and had the fewest artifacts, supporting its continued use during laparoscopic procedures.

Effects of Progesterone on Preclinical Animal Models of Traumatic Brain Injury: Systematic Review and Meta-analysis.

Since the publication of two phase III clinical trials not supporting the use of progesterone in patients with traumatic brain injury (TBI), several possible explanations have been postulated, including limitations in the analysis of results from preclinical evidence. Therefore, to address this question, a systematic review and meta-analysis was performed to evaluate the effects of progesterone as a neuroprotective agent in preclinical animal models of TBI. A total of 48 studies were included for review: 29 evaluated brain edema, 21 evaluated lesion size, and 0 studies reported the survival rate. In the meta-analysis, it was found that progesterone reduced brain edema (effect size - 1.73 [- 2.02, - 1.44], p < 0.0001) and lesion volume (effect size - 0.40 [- 0.65, - 0.14], p = 0.002). Lack of details in the studies hindered the assessment of risk of bias (through the SYRCLE tool). A funnel plot asymmetry was detected, suggesting a possible publication bias. In conclusion, preclinical studies show that progesterone has an anti-edema effect in animal models of TBI, decreasing lesion volume or increasing remaining tissue. However, more studies are needed using assessing methods with lower risk of histological artifacts.

Measuring the Submucosal Depth of Invasion in Endoscopic Mucosal Resections for Barrett-associated Adenocarcinoma: Practical Issues and Relevance for the Decision for Esophagectomy.

Endoscopic mucosal resection (EMR) has made it possible for Barrett esophagus patients with superficial cancers to be treated without esophagectomy. Recent guidelines recommend measuring depth of invasion (DOI) in submucosal cancers based on reports that in low-risk cancers, submucosal invasion 500 μm or less is associated with low nodal metastasis rates. However, pathologists face challenges in reproducibly measuring DOI. To determine how often DOI measurements could impact treatment and to evaluate reproducibility in measuring submucosal DOI in EMR specimens. Consecutive adenocarcinoma EMR cases were identified, including cases of "low histologic risk" submucosal cancer, as follows: those with negative deep margins, no high-grade histology (G3), and no lymphovascular invasion. Submucosal DOI was measured by 7 pathologists according to guidelines. Of 213 cancer EMR cases, 46 were submucosa invasive and 6 cases were low histologic risk submucosal cancers for which measurement could impact decision-making. Of these low histologic risk cases, 3 were categorized as superficial, indicating that measurement would be a clinically actionable decision point in only 1.4% of adenocarcinoma EMRs. Interobserver agreement for in-depth categorization between 7 pathologists was moderate (κ = 0.42), and the range of measurements spanned the 500-μm relevant threshold in 40 of 55 measured samples (72.7%). While therapeutic decisions would rarely have depended on DOI measurements alone in our cohort, interobserver variability raises concerns about their use as a sole factor on which to offer patients conservative therapy. Responsibly reporting and clinically using submucosal DOI measurements will require practical experience troubleshooting common histologic artifacts, as well as multidisciplinary awareness of the impact of variable specimen-handling practices.

Aspectos anatomopatológicos e o uso da imuno-histoquímica em suínos abatidos com lesões cutâneas de erisipela

ABSTRACT: Swine erysipelas is a disease of worldwide distribution, responsible for causing economic losses in swine and considered an occupational zoonotic disease. It is estimated that 30% to 50% of pigs are carriers and stress can predispose the appearance of clinical disease. The diagnosis of erysipelas in slaughter pigs becomes a challenge for pathologists, since scalding and dehairing, routine procedures in slaughterhouses, generate histological artifacts that often make the final diagnosis impossible. This study describes the anatomopathological aspects and evaluate the use of immunohistochemistry as a diagnostic tool in these cases. Forty-three cases of erysipelas in slaughter pigs were analyzed. Grossly, the cutaneous lesions were characteristic pink, red, or purple raised rhomboid, rectangular or square lesions (“diamond skin”). Histologically, in the dermis and subcutaneous tissue, there were suppurative vasculitis, hidradenitis and folliculitis, as well as degeneration and necrosis of the vessel wall, thrombosis and multifocal areas of necrosis. Suppurative vasculitis and damage to the blood vessel wall were observed in all cases, with varying degrees of severity. The immunohistochemical technique proved to be an effective complementary method of diagnosis, with positive immunostaining in 93%. In most cases, we observed mild immunostaining (57.5%), moderate in 22.5% and marked in 20%.

Quality control stress test for deep learning-based diagnostic model in digital pathology

Digital pathology provides a possibility for computational analysis of histological slides and automatization of routine pathological tasks. Histological slides are very heterogeneous concerning staining, sections' thickness, and artifacts arising during tissue processing, cutting, staining, and digitization. In this study, we digitally reproduce major types of artifacts. Using six datasets from four different institutions digitized by different scanner systems, we systematically explore artifacts' influence on the accuracy of the pre-trained, validated, deep learning-based model for prostate cancer detection in histological slides. We provide evidence that any histological artifact dependent on severity can lead to a substantial loss in model performance. Strategies for the prevention of diagnostic model accuracy losses in the context of artifacts are warranted. Stress-testing of diagnostic models using synthetically generated artifacts might be an essential step during clinical validation of deep learning-based algorithms.

Convolutional neural networks for cytoarchitectonic brain mapping at large scale

Human brain atlases provide spatial reference systems for data characterizing brain organization at different levels, coming from different brains. Cytoarchitecture is a basic principle of the microstructural organization of the brain, as regional differences in the arrangement and composition of neuronal cells are indicators of changes in connectivity and function. Automated scanning procedures and observer-independent methods are prerequisites to reliably identify cytoarchitectonic areas, and to achieve reproducible models of brain segregation. Time becomes a key factor when moving from the analysis of single regions of interest towards high-throughput scanning of large series of whole-brain sections. Here we present a new workflow for mapping cytoarchitectonic areas in large series of cell-body stained histological sections of human postmortem brains. It is based on a Deep Convolutional Neural Network (CNN), which is trained on a pair of section images with annotations, with a large number of un-annotated sections in between. The model learns to create all missing annotations in between with high accuracy, and faster than our previous workflow based on observer-independent mapping. The new workflow does not require preceding 3D-reconstruction of sections, and is robust against histological artefacts. It processes large data sets with sizes in the order of multiple Terabytes efficiently. The workflow was integrated into a web interface, to allow access without expertise in deep learning and batch computing. Applying deep neural networks for cytoarchitectonic mapping opens new perspectives to enable high-resolution models of brain areas, introducing CNNs to identify borders of brain areas.

Current knowledge on the immune microenvironment and emerging immunotherapies in diffuse midline glioma.

Diffuse midline glioma (DMG) is an incurable malignancy with the highest mortality rate among pediatric brain tumors. While radiotherapy and chemotherapy are the most common treatments, these modalities have limited promise. Due to their diffuse nature in critical areas of the brain, the prognosis of DMG remains dismal. DMGs are characterized by unique phenotypic heterogeneity and histological features. Mutations of H3K27M, TP53, and ACVR1 drive DMG tumorigenesis. Histological artifacts include pseudopalisading necrosis and vascular endothelial proliferation. Mouse models that recapitulate human DMG have been used to study key driver mutations and the tumor microenvironment. DMG consists of a largely immunologically cold tumor microenvironment that lacks immune cell infiltration, immunosuppressive factors, and immune surveillance. While tumor-associated macrophages are the most abundant immune cell population, there is reduced T lymphocyte infiltration. Immunotherapies can stimulate the immune system to find, attack, and eliminate cancer cells. However, it is critical to understand the immune microenvironment of DMG before designing immunotherapies since differences in the microenvironment influence treatment efficacy. To this end, our review aims to overview the immune microenvironment of DMG, discuss emerging insights about the immune landscape that drives disease pathophysiology, and present recent findings and new opportunities for therapeutic discovery.

Histological effect caused by contrast solution injection for post mortem computed tomography angiography in dogs

Abstract The post mortem computed tomography angiography (PMCTA) is a technique that uses a contrast solution to evaluate the vascular structures in cadavers. This study aims to verify if there is any tissue impairment in parenchymatous organs after PMCTA in dogs. PMCTA was performed in 9 cadavers, divided into 3 groups. There is 23% volemia of contrast solution in groups 1 and 2, and 46% in group 3. Iodine contrast was diluted in polyethylene glycol in groups 1 and 3, and in soybean oil in group 2. Tissue samples were collected from lungs, liver and kidney before and after the PMCTA. The contrast perfusion of each target-organ was measured through CT images by the increased attenuation of Hounsfield units. Each histological sample was evaluated according to its correspondence with the sampling organ and its quality. The presence of artifacts was also assessed and the histological findings were described. The sample quality was attributed a score between 0 and 2. The histological findings were compared for samples collected before and after the PMCTA procedure, and the similarity degree for each pair was calculated. The means of attenuation increase, quality score, and similarity degree were 53, 31 and 157 HU; 1.6, 1.9 and 1.5; and 67%, 62% and 56% for groups 1,2 and 3 respectively. No histological artifact or impairment was noticed in the histological evaluation of samples collected after PMCTA. Therefore, it can be concluded that histological evaluation can be performed after PMCTA to support the post mortem diagnosis.

Pinch biopsy: A modified punch biopsy technique to avoid histological artifacts and surgical tools.

Pinch biopsy: A modified punch biopsy technique to avoid histological artifacts and surgical tools.

A simple method defines 3D morphology and axon projections of filled neurons in a small CNS volume: Steps toward understanding functional network circuitry

BackgroundFundamental to understanding neuronal network function is defining neuron morphology, location, properties, and synaptic connectivity in the nervous system. A significant challenge is to reconstruct individual neuron morphology and connections at a whole CNS scale and bring together functional and anatomical data to understand the whole network. New MethodWe used a PC controlled micropositioner to hold a fixed whole mount of Xenopus tadpole CNS and replace the stage on a standard microscope. This allowed direct recording in 3D coordinates of features and axon projections of one or two neurons dye-filled during whole-cell recording to study synaptic connections. Neuron reconstructions were normalised relative to the ventral longitudinal axis of the nervous system. Coordinate data were stored as simple text files. ResultsReconstructions were at 1 μm resolution, capturing axon lengths in mm. The output files were converted to SWC format and visualised in 3D reconstruction software NeuRomantic. Coordinate data are tractable, allowing correction for histological artefacts. Through normalisation across multiple specimens we could infer features of network connectivity of mapped neurons of different types. Comparison with Existing MethodsUnlike other methods using fluorescent markers and utilising large-scale imaging, our method allows direct acquisition of 3D data on neurons whose properties and synaptic connections have been studied using whole-cell recording. ConclusionsThis method can be used to reconstruct neuron 3D morphology and follow axon projections in the CNS. After normalisation to a common CNS framework, inferences on network connectivity at a whole nervous system scale contribute to network modelling to understand CNS function.

Regional registration of whole slide image stacks containing major histological artifacts

BackgroundHigh resolution 2D whole slide imaging provides rich information about the tissue structure. This information can be a lot richer if these 2D images can be stacked into a 3D tissue volume. A 3D analysis, however, requires accurate reconstruction of the tissue volume from the 2D image stack. This task is not trivial due to the distortions such as tissue tearing, folding and missing at each slide. Performing registration for the whole tissue slices may be adversely affected by distorted tissue regions. Consequently, regional registration is found to be more effective. In this paper, we propose a new approach to an accurate and robust registration of regions of interest for whole slide images. We introduce the idea of multi-scale attention for registration.ResultsUsing mean similarity index as the metric, the proposed algorithm (mean ± SD 0.84 pm 0.11) followed by a fine registration algorithm (0.86 pm 0.08) outperformed the state-of-the-art linear whole tissue registration algorithm (0.74 pm 0.19) and the regional version of this algorithm (0.81 pm 0.15). The proposed algorithm also outperforms the state-of-the-art nonlinear registration algorithm (original: 0.82 pm 0.12, regional: 0.77 pm 0.22) for whole slide images and a recently proposed patch-based registration algorithm (patch size 256: 0.79 pm 0.16 , patch size 512: 0.77 pm 0.16) for medical images.ConclusionUsing multi-scale attention mechanism leads to a more robust and accurate solution to the problem of regional registration of whole slide images corrupted in some parts by major histological artifacts in the imaged tissue.

Minimizing shrinkage of acute brain slices using metal spacers during histological embedding

The morphological structure of neurons provides the basis for their functions and is a major focus of contemporary neuroscience studies. Intracellular staining of single cells in acute slices is a well-established approach, offering high-resolution information on neuronal morphology, complementing their physiology. Despite major technical advances, however, a common histological artifact often precludes precise morphological analysis: shrinkage of the sampled tissue after embedding for microscopy. Here, we describe a new approach using a metal spacer, sandwiched between two coverslips to reduce shrinkage of whole-mount slice preparations during embedding with aqueous mounting medium under a coverslip. This approach additionally allows imaging the slices from both sides to obtain better quality images of deeper structures. We demonstrate that the use of this spacer system can efficiently and stably reduce the shrinkage of slices, whereas conventional embedding methods without spacer or with agar spacer cause severe, progressive shrinkage after embedding. We further show that the shrinkage of slices is not uniform and artifacts in morphology and anatomical parameters produced cannot be compensated using linear correction algorithms. Our study, thus, emphasizes the importance of preventing the deformation of slice preparations and offers an effective means for reducing shrinkage and associated artifacts during embedding.

Nankeen ink model for histological distribution of solutions used in post mortem CT-angiography

• It was possible to identify impregnation in capilar lumen on histological slices. • Nankeen ink allow histological distribution evaluation of the contrast used in PMCTA. • PEG and contrast mixtures reached the minor vessels of all the evaluated organs. • Soybean oil and contrast mixtures reached the minor vessels of all the evaluated organs. • No artifacts or histological damages were seen after the mixture injection. Post mortem computed tomography angiography (PMCTA) is an imaging modality that uses several different contrast solutions in order to highlight blood vessel paths in cadavers. This technique shows similar results when compared to conventional necropsy, especially for traumatic or vascular diseases. However, it is still unknown whether the chemical and histological features remain preserved after the intravascular injection of contrast solution for PMCTA. The aim of this study was to establish the histological regions reached by the contrast medium solution after a PMCTA procedure and to verify if the tissue architecture was preserved, using two different types of fluids to compose the solution (watery and oil fluid). A nankeen ink model was used in 2 dog cadavers with 2 different contrast solution, and a histological evaluation of the lung, liver and kidney was carried out. Nankeen ink impregnation was observed in all samples collected after the mixture injection showing the presence of ink impregnation within the blood vessel lumens. No histological artifacts were found and, moreover, histological architecture damages were not observed in those samples collected. It had been demonstrated that this nankeen ink model can be used for further studies in due to better understand the histological distribution of the contrast solution used in PMCTA procedures.