scholarly journals An image dataset related to automated macrophage detection in immunostained lymphoma tissue samples

GigaScience ◽  
2020 ◽  
Vol 9 (3) ◽  
Author(s):  
Marcus Wagner ◽  
Sarah Reinke ◽  
René Hänsel ◽  
Wolfram Klapper ◽  
Ulf-Dietrich Braumann
Keyword(s):  
Reference Method ◽  
Image Data ◽  
B Cell Lymphoma ◽  
Automated Image Analysis ◽  
Large Set ◽  
Cell Nuclei ◽  
Tissue Samples ◽  
Automated Recognition ◽  
Tissue Sections ◽  
Image Dataset

Abstract Background We present an image dataset related to automated segmentation and counting of macrophages in diffuse large B-cell lymphoma (DLBCL) tissue sections. For the classification of DLBCL subtypes, as well as for providing a prognosis of the clinical outcome, the analysis of the tumor microenvironment and, particularly, of the different types and functions of tumor-associated macrophages is indispensable. Until now, however, most information about macrophages has been obtained either in a completely indirect way by gene expression profiling or by manual counts in immunohistochemically (IHC) fluorescence-stained tissue samples while automated recognition of single IHC stained macrophages remains a difficult task. In an accompanying publication, a reliable approach to this problem has been established, and a large set of related images has been generated and analyzed. Results Provided image data comprise (i) fluorescence microscopy images of 44 multiple immunohistostained DLBCL tumor subregions, captured at 4 channels corresponding to CD14, CD163, Pax5, and DAPI; (ii) ”cartoon-like” total variation–filtered versions of these images, generated by Rudin-Osher-Fatemi denoising; (iii) an automatically generated mask of the evaluation subregion, based on information from the DAPI channel; and (iv) automatically generated segmentation masks for macrophages (using information from CD14 and CD163 channels), B-cells (using information from Pax5 channel), and all cell nuclei (using information from DAPI channel). Conclusions A large set of IHC stained DLBCL specimens is provided together with segmentation masks for different cell populations generated by a reference method for automated image analysis, thus featuring considerable reuse potential.

Three-dimensional light microscopy, optimized staining, and automated image analysis of cell nuclei in thick tissue slices

1993 ◽  
Vol 51 ◽  
pp. 268-269 ◽  
Author(s):  
W. Lin ◽  
T. Holmes ◽  
H. Ancin ◽  
B. Roysam ◽  
D.H. Szarowski ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Brain Slices ◽  
Tissue Level ◽  
Automated Image Analysis ◽  
Cell Nuclei ◽  
Tissue Slices ◽  
Tissue Samples ◽  
Schiff Reagent ◽  
And Function ◽  
Spatial Locations

The number, size, shape and three-dimensional (3D) distribution of cell nuclei in thick tissue samples is often critical to our understanding of tissue level organization and function. Examples include the analysis of neurons in brain tissue as a function of development, electrical activity, and exposure to toxins as well as the development of whole embryos. The sample is stained with a fluorescent dye selective for nucleic acid, and observed with a confocal light microscope. The classic Feulgen stain, although primarily an absorption stain, is often used for this purpose. However, it is unreliable for fluorescence due to the mixture of compounds usually present in Fuchsin. We have optimized a procedure using acriflavine as the Schiff reagent for staining thick (100 - 500 μm) brain slices. In addition, Ancin and Roysam have developed software for automatically analyzing 3D objects, which are classified by volume, shape, intensity and relative 3D spatial locations.

scholarly journals Assessment of Global Methylation in Paraffin Embedded Prostatic Tissues and Cell Lines Using Flow Cytometry

2018 ◽  
Vol 1 (1) ◽  
pp. 34-38
Author(s):  
Osama Sharaf Eldin ◽  
Mahmoud M. Elfar ◽  
Abdel-Motaal Fouda
Keyword(s):  
Flow Cytometry ◽  
Cell Lines ◽  
Objective Assessment ◽  
Prostate Adenocarcinoma ◽  
Cell Nuclei ◽  
Global Methylation ◽  
Tissue Samples ◽  
Tissue Sections ◽  
Global Hypomethylation ◽  
Prostatic Cell

Background. The aim of this study is to measure global 5-methylcystosine (5MeC) methylation in paraffin embedded prostatic tissues and cell lines using flow cytometry. Methods. Cell/nuclei suspension from 10 cases of benign prostatic hyperplasia (BPH), 10 cases of prostatic adenocarcinoma, and two prostatic cell lines (PNT1A and LNCaP) were prepared using modified heat pretreatment technique. 5MeC global methylation was assessed by flow cytometry of cell/nuclei suspension and immunostaining of tissue sections. Results. Higher percentage of positively stained cells (PPSC) and mean channel fluorescence (MCF) were detected in PNT1A cell line and BPH cell/nuclei suspensions as compared to LNCaP cell lines and adenocarcinoma cell/nuclei suspensions. Lower scores of 5MeC immunostaining were observed in all prostate adenocarcinoma tissue sections as compared to BPH sections indicating global hypomethylation in prostate adenocarcinoma. Two distinctive populations of cells were detected in histograms generated from most of the BPH cell/nuclei suspensions. Conclusion. The study developed a novel technique that could measure 5MeC global methylation in paraffin embedded prostatic tissues. This represents a rapid and objective assessment of methylation and when combined with tissue micro-dissection and cell sorting, this technique could be applied to larger tissue samples such as post radical prostatectomy and transurethral resected specimens.

Discovery of intracellular 2,8 dihydroxyadenine crystals in bovine lymphatic and hepatic cells

1987 ◽  
Vol 45 ◽  
pp. 906-907
Author(s):  
W. E. Rigsby ◽  
D. M. Hinton ◽  
V. J. Hurst ◽  
P. C. McCaskey
Keyword(s):  
Polarized Light ◽  
Paraffin Sections ◽  
Tissue Samples ◽  
Whole Cells ◽  
Tissue Sections ◽  
Hepatic Cells ◽  
Slaughter House ◽  
Mammalian Tissues ◽  
Carbon Coated ◽  
Cellular Components

Crystalline intracellular inclusions are rarely seen in mammalian tissues and are often difficult to positively identify. Lymph node and liver tissue samples were obtained from two cows which had been rejected at the slaughter house due to the abnormal appearance of these organs in the animals. The samples were fixed in formaldehyde and some of the fixed material was embedded in paraffin. Examination of the paraffin sections with polarized light microscopy revealed the presence of numerous crystals in both hepatic and lymph tissue sections. Tissue sections were then deparaffinized in xylene, mounted, carbon coated, and examined in a Phillips 505T SEM equipped with a Tracor Northern X-ray Energy Dispersive Spectroscopy (EDS) system. Crystals were obscured by cellular components and membranes so that EDS spectra were only obtainable from whole cells. Tissue samples which had been fixed but not paraffin-embedded were dehydrated, embedded in Spurrs plastic, and sectioned.

scholarly journals Rapid brain structure and tumour margin detection on whole frozen tissue sections by fast multiphotometric mid-infrared scanning

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tim Kümmel ◽  
Björn van Marwick ◽  
Miriam Rittel ◽  
Carina Ramallo Guevara ◽  
Felix Wühler ◽  
...  
Keyword(s):  
Imaging System ◽  
Frozen Section ◽  
Computational Effort ◽  
Primary Hepatocellular Carcinoma ◽  
Measuring System ◽  
Sufficient Information ◽  
Tissue Samples ◽  
Mid Infrared ◽  
Tissue Sections ◽  
Frozen Tissue

AbstractFrozen section analysis is a frequently used method for examination of tissue samples, especially for tumour detection. In the majority of cases, the aim is to identify characteristic tissue morphologies or tumour margins. Depending on the type of tissue, a high number of misdiagnoses are associated with this process. In this work, a fast spectroscopic measurement device and workflow was developed that significantly improves the speed of whole frozen tissue section analyses and provides sufficient information to visualize tissue structures and tumour margins, dependent on their lipid and protein molecular vibrations. That optical and non-destructive method is based on selected wavenumbers in the mid-infrared (MIR) range. We present a measuring system that substantially outperforms a commercially available Fourier Transform Infrared (FT-IR) Imaging system, since it enables acquisition of reduced spectral information at a scan field of 1 cm2 in 3 s, with a spatial resolution of 20 µm. This allows fast visualization of segmented structure areas with little computational effort. For the first time, this multiphotometric MIR system is applied to biomedical tissue sections. We are referencing our novel MIR scanner on cryopreserved murine sagittal and coronal brain sections, especially focusing on the hippocampus, and show its usability for rapid identification of primary hepatocellular carcinoma (HCC) in mouse liver.

Visualisation of GABAergic neurons and synapses in the rat brain using immunohistochemistry for two forms of glutamate decarboxylase

2021 ◽  
Vol 21 (2) ◽  
pp. 63-73
Author(s):  
Valeria A. Razenkova ◽  
Dmitrii E. Korzhevskii
Keyword(s):  
Brain Tissue ◽  
Glutamate Decarboxylase ◽  
Brain Structures ◽  
Gabaergic Neurons ◽  
Laboratory Animals ◽  
Tissue Samples ◽  
Tissue Sections ◽  
Background Staining ◽  
The Central Nervous System ◽  
Rat Forebrain

BACKGROUND: Taking into account the importance of GABAergic brain system research and also the opportunity to achieve specific and accurate results in laboratory studies using immunohistochemical approaches, it seems important to have a reliable method of visualization GABA-synthesizing cells, their projections and synapses, for the morphofunctional analysis of GABAergic system both in normal conditions and in the experimental pathology. AIM: The aim of the study was to visualize analyze GABAergic neurons and synapses within rats brain using three different antibody types against glutamate decarboxylase and to identify the optimal conditions for reaction performing. MATERIALS AND METHODS: The study was performed on paraffin brain tissue sections of 5 adult Wistar rats. Immunohistochemical reactions using three antibody types against glutamate decarboxylase isoform 67 (GAD67) and glutamate decarboxylase isoform 65 (GAD65) were performed. Additional controls on C57/Bl6 mice and Chinchilla rabbits brain samples were also carried out. RESULTS: Antibodies used in the research made it possible to achieve high quality of GABAergic structures visualizing without increasing background staining. At the same time different antibody types are distinct in their efficacy to perform immunohistochemistry reaction on laboratory animal brain tissue samples. By performing additional controls, we discovered that there is necessary to adsorb secondary reagents immunoglobulins in order to eliminate nonspecific staining. It was found that GAD67 and GAD65 distribution in rat forebrain structures is different. It was stated that GAD67 immunohistochemistry most completely reveals GABAergic brain structures compared to GAD65 immunhistochemistry. The possibility of determining morphological features of GABAergic neurons and synaptic terminals, as well as performing quantitative analysis, was demonstrated. CONCLUSIONS: The approach proposed makes it possible to specifically visualize GABAergic structures of the central nervous system of different laboratory animals. This could be useful both in fundamental studies and in pathology research.

Rapid Somatic Mutation Testing in Colorectal Cancer by Use of a Fully Automated System and Single-Use Cartridge: A Comparison with Next-Generation Sequencing

2018 ◽  
Vol 3 (2) ◽  
pp. 178-184 ◽  
Author(s):  
M Rabie Al-Turkmani ◽  
Kelley N Godwin ◽  
Jason D Peterson ◽  
Gregory J Tsongalis
Keyword(s):  
Colorectal Cancer ◽  
Next Generation Sequencing ◽  
Ffpe Tissue ◽  
Braf V600e ◽  
Automated System ◽  
Next Generation ◽  
Tissue Samples ◽  
Tissue Sections ◽  
Single Use ◽  
Generation Sequencing

AbstractBackgroundMolecular tests have been increasingly used in the management of various cancers as more targeted therapies are becoming available as treatment options. The Idylla™ system is a fully integrated, cartridge-based platform that provides automated sample processing (deparaffinization, tissue digestion, and DNA extraction) and real-time PCR-based mutation detection with all reagents included in a single-use cartridge. This retrospective study aimed at evaluating both the Idylla KRAS and NRAS-BRAF-EGFR492 Mutation Assay cartridges (research use only) against next-generation sequencing (NGS) by using colorectal cancer (CRC) tissue samples.MethodsForty-four archived formalin-fixed paraffin-embedded (FFPE) CRC tissue samples previously analyzed by targeted NGS were tested on the Idylla system. Among these samples, 17 had a mutation in KRAS proto-oncogene, GTPase (KRAS), 5 in NRAS proto-oncogene, GTPase (NRAS), and 12 in B-Raf proto-oncogene, serine/threonine kinase (BRAF) as determined using the Ion AmpliSeq 50-gene Cancer Hotspot Panel v2. The remaining 10 samples were wild-type for KRAS, NRAS, and BRAF. Two 10-μm FFPE tissue sections were used for each Idylla run, 1 for the KRAS cartridge, and 1 for the NRAS-BRAF-EGFR492 cartridge. All cases met the Idylla minimum tumor content requirement for KRAS, NRAS, and BRAF (≥10%). Assay reproducibility was evaluated by testing commercial controls derived from human cell lines, which had an allelic frequency of 50% and were run in triplicate.ResultsThe Idylla system successfully detected all mutations previously identified by NGS in KRAS (G12C, G12D, G12V, G13D, Q61K, Q61R, A146T), NRAS (G12V, G13R, Q61H), and BRAF (V600E). Compared with NGS, Idylla had a sensitivity of 100%. Analysis of the mutated commercial controls demonstrated agreement with the expected result for all samples and 100% reproducibility. The Idylla system produced results quickly with a turnaround time of approximately 2 h.ConclusionThe Idylla system offers reliable and sensitive testing of clinically actionable mutations in KRAS, NRAS, and BRAF directly from FFPE tissue sections.

scholarly journals First evidence of nocardiosis in farmed red drum (Sciaenops ocellatus, Linnaeus) caused by Nocardia seriolae in the Gulf of Mexico

2021 ◽  
Author(s):  
Rodolfo Enrique del Rio-Rodriguez ◽  
Jose Gustavo Ramirez-Paredes ◽  
Sonia Araceli Soto-Rodriguez ◽  
Yechiam Shapira ◽  
Mariana del Jesus Huchin-Cortes ◽  
...  
Keyword(s):  
Current Knowledge ◽  
Red Drum ◽  
Sciaenops Ocellatus ◽  
Internal Organs ◽  
New Host ◽  
Tissue Samples ◽  
Tissue Sections ◽  
Long Rod ◽  
Nocardia Seriolae

ABSTRACTBetween August and December 2013, the offshore cages of a commercial marine farm culturing red drum Sciaenops ocellatus in Campeche Bay were affected by an outbreak of an ulcerative granulomatous disease, reaching 70% cumulative mortality. Thirty-one adults displaying open ulcers on the skin were submitted to our laboratory for diagnosis. Multiple white-yellowish nodules (0.1-0.5 cm in diameter) were present in all internal organs, where the kidney and the spleen were the most severely affected. Histopathological observations of these organs evinced typical granulomatous formations. Gram and Ziehl-Neelsen stains on tissue imprints, bacterial swabs and tissue sections revealed Gram-positive, acid-fast, branching beaded long rod filamentous bacteria. Tissue samples resulted positive for nocardiosis when a Nocardia genus specific nested PCR was used. Definite identification at the species level and taxonomic positioning of the fastidious pathogen was achieved through a specific Nocardia seriolae PCR and by sequencing the gyrB gene of pure isolates. After application of antibiotics during fry production, a posterior follow-up monitoring (from 2014 to 2017) detected mild but recurrent outbreaks of the bacteria with no seasonality pattern. To the extent of our current knowledge, this is the first report of piscine nocardiosis (in a new host -red drum) in Mexico.

Crisp and soft multivariate methods visualize individual cell nuclei in Raman images of liver tissue sections

2011 ◽  
Vol 55 (1) ◽  
pp. 90-100 ◽  
Author(s):  
Christoph Krafft ◽  
Mehrnaz Alipour Diderhoshan ◽  
Peter Recknagel ◽  
Milos Miljkovic ◽  
Michael Bauer ◽  
...  
Keyword(s):  
Liver Tissue ◽  
Individual Cell ◽  
Multivariate Methods ◽  
Cell Nuclei ◽  
Tissue Sections

scholarly journals High-throughput microfluidic micropipette aspiration device to probe time-scale dependent nuclear mechanics in intact cells

Lab on a Chip ◽  
2019 ◽  
Vol 19 (21) ◽  
pp. 3652-3663 ◽  
Author(s):  
Patricia M. Davidson ◽  
Gregory R. Fedorchak ◽  
Solenne Mondésert-Deveraux ◽  
Emily S. Bell ◽  
Philipp Isermann ◽  
...  
Keyword(s):  
Image Analysis ◽  
High Throughput ◽  
Time Scale ◽  
Viscoelastic Properties ◽  
Micropipette Aspiration ◽  
Automated Image Analysis ◽  
Cell Nuclei ◽  
Intact Cells ◽  
Nuclear Mechanics ◽  
Analysis Platform

We report the development, validation, and application of an easy-to-use microfluidic micropipette aspiration device and automated image analysis platform that enables high-throughput measurements of the viscoelastic properties of cell nuclei.

Wear debris from hip prostheses characterized by electron imaging

Open Medicine ◽  
2013 ◽  
Vol 8 (4) ◽  
pp. 476-484 ◽  
Author(s):  
Matevž Topolovec ◽  
Ingrid Milošev ◽  
Andrej Cör ◽  
Roy Bloebaum
Keyword(s):  
Spatial Relationship ◽  
Particle Identification ◽  
Submicron Particles ◽  
Metal Particles ◽  
Wear Particles ◽  
Scattered Electron ◽  
Tissue Samples ◽  
Tissue Sections ◽  
Electron Imaging

AbstractThe characterization of wear particles is of great importance in understanding the mechanisms of osteolysis. In this unique study, thirty-one tissue samples were retrieved at revision surgeries of hip implants and divided into four groups according to the composition of metal prosthetic components. Tissue samples were first analyzed histologically and then by scanning electron microscopy (SEM) combined with back-scattered electron imaging and energy dispersive X-ray spectroscopy. Therefore, particles were studied directly in situ in tissue sections, without the requirement for particle isolation. The composition of metal wear particles detected in the tissue sections corresponded to the composition of the implant components. A considerable number of large metal particles were actually clusters of submicron particles. The clustering of submicron particles was observed primarily with CoCrMo (cobalt-chromiummolybdenum) and, to a lesser extent, for stainless steel particles. SEM secondary and back-scattered electron imaging was an appropriate and selective method for recognizing the composition of metal particles in the in situ tissue sections, without destroying their spatial relationship within the histology. This method can be used as a screening tool for composition of metal and ceramic particles in tissue sections, or as an additional method for particle identification.

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