A CNN-based approach for joint segmentation and quantification of nuclei and NORs in AgNOR-stained images.

BACKGROUND AND OBJECTIVE: Oral cancer is the sixth most common kind of human cancer. Brush cytology for counting Argyrophilic Nucleolar Organizer Regions (AgNORs) can help early mouth cancer detection, lowering patient mortality. However, the manual counting of AgNORs still in use today is time-consuming, labor-intensive, and error-prone. The goal of our work is to address these shortcomings by proposing a convolutional neural network (CNN) based method to automatically segment individual nuclei and AgNORs in microscope slide images and count the number of AgNORs within each nucleus. METHODS: We systematically defined, trained and tested 102 CNNs in the search for a high-performing solution. This included the evaluation of 51 network architectures combining 17 encoders with 3 decoders and 2 loss functions. These CNNs were trained and evaluated on a new AgNOR-stained image dataset of epithelial cells from oral mucosa containing 1,171 images from 48 patients, with ground truth annotated by specialists. The annotations were greatly facilitated by a semi-automatic procedure developed in our project. Overlapping nuclei, which tend to hide AgNORs, thus affecting their true count, were discarded using an automatic solution also developed in our project. Besides the evaluation on the test dataset, the robustness of the best performing model was evaluated against the results produced by a group of human experts on a second dataset. RESULTS: The best performing CNN model on the test dataset consisted of a DenseNet-169 + LinkNet with Focal Loss (DenseNet-169 as encoder and LinkNet as decoder). It obtained a Dice score of 0.90 and intersection over union (IoU) of 0.84. The counting of nuclei and AgNORs achieved precision and recall of 0.94 and 0.90 for nuclei, and 0.82 and 0.74 for AgNORs, respectively. Our solution achieved a performance similar to human experts on a set of 291 images from 6 new patients, obtaining Intraclass Correlation Coefficient (ICC) of 0.91 for nuclei and 0.81 for AgNORs with 95% confidence intervals of [0.89, 0.93] and [0.77, 0.84], respectively, and p-values < 0.001, confirming its statistical significance. Our AgNOR-stained image dataset is the most diverse publicly available AgNOR-stained image dataset in terms of number of patients and the first for oral cells. CONCLUSIONS: CNN-based joint segmentation and quantification of nuclei and NORs in AgNOR-stained images achieves expert-like performance levels, while being orders of magnitude faster than the later. Our solution demonstrated this by showing strong agreement with the results produced by a group of specialists, highlighting its potential to accelerate diagnostic workflows. Our trained model, code, and dataset are available and can stimulate new research in early oral cancer detection.

Golgi Silver Staining of Mosquito Central Neuropils.

The Golgi silver staining procedure relies on three interdependent stages: fixation, chromation, and metal impregnation. Each of these stages can be modified. This protocol describes a method demonstrated to stain neurons within the mosquito central nervous system. The resulting preparations are stable at room temperature.

The Golgi Method.

Silver staining by the Golgi method is a classical procedure to identify the three-dimensional morphology of individual neurons. Although the method was developed in the 1870s, it is still used to study the morphological characteristics of neuron types in the central nervous system, either alone or in combination with other neuroanatomical techniques. The neuropil of insects is fully accessible to the original refractive staining procedure, and modifications of the Golgi technique have paved the path for modern structural research on the insect central nervous system. Here, we provide an introduction to this easy and low-cost method.

Adapted technique for demonstrating argyrophilic nucleolar organizer regions in the cytologic samples of canine mast cell tumors.

INTRODUCTION: Argyrophilic nucleolar organizer regions (AgNORs) are nonhistone argyrophilic nucleolar proteins associated with ribosomal genes found in the nucleolar organizer region that reflect cell proliferation and have an affinity for silver. AgNOR staining may be useful to evaluate prognosis in several neoplasms because higher AgNOR counts are related to higher grade tumors, metastases, and shorter survival times. OBJECTIVE: We aimed to report on a quick and practical technique to identify AgNORs adapted for use in routine cytology. MATERIALS AND METHODS: The cytopathologic diagnosis of mast cell tumor (MCT) in samples collected by fine-needle aspiration (FNA) was determined. Next, slides were impregnated with a solution containing silver nitrate; the main modification of our technique included incubation of these slides at a controlled temperature of 25 °C. Some slides were previously stained with Diff-Quik and others were only fixed with methanol. The slides were analyzed under a microscope, and the number of blackened intranuclear points (AgNORs) was counted. RESULTS: Slides prestained with Diff-Quik were easily counted compared with slides only fixed in methanol. Technical issues encountered with the methanol-fixed slides included insufficient cellularity, background precipitation, and an absence of silver impregnation. CONCLUSIONS: The technique reported in this study showed satisfactory results for AgNOR counting in cytologic smears from MCT, such as good impregnation and the elimination of background interferents. Further evaluation of this method comparing AgNOR counts with histologic examinations, tumor grades, other prognostic markers, and survival times are needed to fully evaluate the benefit of this technique.

Staining Sodium Dodecyl Sulfate-Polyacrylamide Gels with Silver Salts.

This protocol describes silver staining procedures to detect low-abundance proteins in sodium dodecyl sulfate-polyacrylamide gels.

Whole-organism 3D quantitative characterization of zebrafish melanin by silver deposition micro-CT.

We previously described X-ray histotomography, a high-resolution, non-destructive form of X-ray microtomography (micro-CT) imaging customized for three-dimensional (3D), digital histology, allowing quantitative, volumetric tissue and organismal phenotyping (Ding et al., 2019). Here, we have combined micro-CT with a novel application of ionic silver staining to characterize melanin distribution in whole zebrafish larvae. The resulting images enabled whole-body, computational analyses of regional melanin content and morphology. Normalized micro-CT reconstructions of silver-stained fish consistently reproduced pigment patterns seen by light microscopy, and further allowed direct quantitative comparisons of melanin content across wild-type and mutant samples, including subtle phenotypes not previously noticed. Silver staining of melanin for micro-CT provides proof-of-principle for whole-body, 3D computational phenomic analysis of a specific cell type at cellular resolution, with potential applications in other model organisms and melanocytic neoplasms. Advances such as this in whole-organism, high-resolution phenotyping provide superior context for studying the phenotypic effects of genetic, disease, and environmental variables.

Evaluation of sperm morphometry of rabbits (Oryctolagus cuniculus f. domesticus).

Sperm morphology and morphometry are considered parameters in fertility diagnosis. They are especially important in the case of species for which there is no standard with respect to morphometric sperm parameters. It is then crucial to apply the staining technique that has the least influence on the sperm structure and provides the most detailed image, so as to enable measurements. The aim of the research was to assess the morphometric parameters of rabbit sperm using silver nitrate staining. The staining process revealed a detailed image of the spermatozoon head and tail, thus enabling precise measurements. From these basic morphometric parameters, four additional shape indices characterizing the sperm head were calculated: ellipticity, elongation, roughness and regularity. These parameters more precisely characterize the shape of the sperm head. Silver nitrate staining can be used as an independent technique in assessment of sperm structure or to supplement routine diagnostics.

Purification of LPS from Leptospira.

Leptospira species are one of the few spirochetes to possess a lipopolysaccharide (LPS) embedded in their outer membrane. Two protocols are currently available to extract and/or purify the leptospiral lipopolysaccharides: the rapid proteinase K method and the classical hot water/phenol extraction. The first method allows to get a quick overview of the LPS O antigen structure, whereas the second method is fitted to study the immunological properties of the leptospiral LPS. These two methods will be detailed in this chapter. Methodologies to assess the quality of the purification, such as the modified silver staining coloration, will also be reviewed. Both advantages and limitations of the different analyses will be described.

Comparison of the structure of chinchilla sperm isolated from semen and from the tail of the epididymis.

Sperm cells isolated from the tail of the epididymis and from the semen of the same individuals were analysed. The use of silver nitrate to stain sperm cells isolated from the tail of the epididymis made it possible to identify structures that were not visible in the sperm from semen. Silver nitrate very clearly distinguished the acrosomal and distal parts of the sperm head. Following silver nitrate staining, the sperm isolated from the tail of the epididymis were characterized by dark 'collars' in the distal part of the head. These 'collars' are not visible in the sperm cells isolated from semen. The results of the study indicate differences in the dimensions of sperm isolated from the tail of the epididymis and sperm in semen. Sperm isolated from the tail of the epididymis had smaller heads, despite their longer length, and had longer midpieces and tails than ejaculate sperm. Silver nitrate staining is a simple and fast technique. Silver nitrate makes it possible to identify the acrosome and post-acrosomal region of the sperm head and to clearly identify the midpiece. Therefore, it can be successfully used to supplement routine techniques for evaluating sperm morphology or as an independent technique.

Combined Application of Immunohistochemistry and Warthin-Starry Silver Stain on the Pathologic Diagnosis of Cat Scratch Disease.

PURPOSE: Cat scratch disease (CSD) is an infectious disorder caused primarily by the bacterium Bartonella henselae (B. henselae). Immunohistochemistry (IHC) and Warthin-Starry silver stain (WS) are considered to be indispensable to diagnose CSD in combination with morphologic characteristics. In this study, we retrieved and reviewed 46 cases of paraffin-embedded lymphadenitis with histologic and/or clinical suspicion of CSD between 2014 and 2018, and detected B. henselae by IHC and WS, respectively, and evaluated the application significance of IHC and WS for the detection of B. henselae and validated their values in the pathologic diagnosis of CSD. MATERIALS AND METHODS: B. henselae was detected by IHC and WS; validation of 2 methods for detecting B. henselae was evaluated by sensitivity, specificity, false-positive rate, false-negative rate, precision, negative predictive value, and agreement rate. RESULTS: Microscopically, suppurative granulomas and/or multiple stellate microabscesses were observed in the accessory cortex of lymph nodes, especially near the subcapsule. Our results showed that 80.4% (37/46) of cases were positive for B. henselae by IHC, manifesting mainly punctuate, granular, or linear to outline the shape of bacteria. However, the positive rate of B. henselae by the WS method was 52.2% (24/46). There was a significant difference between IHC and WS (P=0.023). Moreover, a positive percentage of B. henselae was 97.8% (45/46), which was detected by the combined application of IHC and WS. The combination of IHC and WS exhibited high sensitivity (97.8%) and good agreement rate (86.5%). CONCLUSION: The combined application of the IHC and WS method may have important clinical advantages, which is with the highest sensitivity and agreement rate for pathologic diagnosis of CSD.

Silver staining (Campbell-Switzer) of neuronal α-synuclein assemblies induced by multiple system atrophy and Parkinson's disease brain extracts in transgenic mice.

Synucleinopathies [Parkinson's disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA)] share filamentous α-synuclein assemblies in nerve cells and glial cells. We compared the abilities of brain extracts from MSA and PD patients to induce neuronal α-synuclein assembly and neurodegeneration following intracerebral injection in heterozygous mice transgenic for human mutant A53T α-synuclein. MSA extracts were more potent than PD extracts in inducing α-synuclein assembly and in causing neurodegeneration. MSA assemblies were Campbell-Switzer- and Gallyas-silver-positive, whereas PD assemblies were only Campbell-Switzer-positive, in confirmation of previous findings. However, induced α-synuclein inclusions were invariably Campbell-Switzer-positive and Gallyas-negative, irrespective of whether MSA or PD brain extracts were injected. The α-synuclein inclusions of non-injected homozygous mice transgenic for A53T α-synuclein were also Campbell-Switzer-positive and Gallyas-negative. These findings demonstrate that transgene expression and its intracellular environment dominated over the silver staining properties of the conformers of assembled α-synuclein.

Golgi-Cox Staining of Neuronal Dendrites and Dendritic Spines With FD Rapid GolgiStain™ Kit.

The Golgi-Cox method has been one of the most effective techniques for studying the morphology of neuronal dendrites and dendritic spines. However, the reliability and time-consuming process of Golgi-Cox staining have been major obstacles to the widespread application of this technique. To overcome these shortcomings and to promote this invaluable technique, we developed the FD Rapid GolgiStain™ Kit based on the principle of the methods described by Ramón-Moliner in 1970 and Glaser and Van der Loos in 1981. The kit significantly improves and simplifies the Golgi-Cox technique. This kit is reliable for visualizing morphological details of neurons, allowing for analysis of various parameters of dendritic morphology-such as dendritic length and branching pattern and dendritic spine number, shape, and size-in both animal and postmortem human brains. A 40-min instructional video for tissue freezing, cryosectioning, and staining is provided. © 2019 by John Wiley & Sons, Inc.

Fluorescent Silver Staining of Proteins in Polyacrylamide Gels.

Silver staining is a colorimetric technique widely used to visualize protein bands in polyacrylamide gels following sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The classic silver stains have certain drawbacks, such as high background staining, poor protein recovery, low reproducibility, a narrow linear dynamic range for quantification, and limited compatibility with mass spectrometry (MS). Now, with the use of a fluorogenic Ag+ probe, TPE-4TA, we developed a fluorescent silver staining method for the total protein visualization in polyacrylamide gels. This new stain avoids the troublesome silver reduction step in traditional silver stains. Moreover, the fluorescent silver stain demonstrates good reproducibility, sensitivity, and linear quantification in protein detection, making it a useful and practical protein gel stain.

Silver-Albumin Tissue Staining Protocol to Visualize Odontogenesis in Whole Embryos.

Visualizing tooth organs from their earliest inception as they actually appear in three dimensions has, until recently, been difficult due to the technical obstacle of imaging these tiny, translucent, low-density embryonic craniodental tissues. Related to this obstacle, quantifying craniodental morphology has been confounded by the time consuming need to physically section and then digitally photograph and reconstruct these images of tissues into 3D volumes. Here we provide a simple solution in the form of an overnight silver albumin tissue stain for whole embryos. Because it is differentially absorbed by embryonic tissues, this stain generates the contrast needed to detect and visualize unmineralized dental tissues. Stained specimens can be scanned using either desktop or synchrotron micro-computed tomography systems, generating digital 3D datasets of whole embryos that can immediately be used to assess dental morphology and histology. Craniodental structures can then be measured with high precision and accuracy using 3D image analysis software.

Immuno-gold silver staining assays on capillary-driven microfluidics for the detection of malaria antigens.

Accurate and affordable rapid diagnostic tests (RDTs) are indispensable but often lacking for many infectious diseases. Specifically, there is a lack of highly sensitive malaria RDTs that can detect low antigen concentration at the onset of infection. Here, we present a strategy to improve the sensitivity of malaria RDTs by using capillary-driven microfluidic chips and combining sandwich immunoassays with electroless silver staining. We used 5 µm fluorescent beads functionalized with capture antibodies (cAbs). These beads are self-assembled by capillary action in recessed "bead lanes", which cross the main flow path of chips microfabricated in Si and SU-8. The binding of analytes to detection antibodies (dAbs) and secondary antibodies (2ndAbs) conjugated to gold nanoparticles (NPs) allows the formation of a silver film on the beads. Such silver film masks the fluorescent core of the bead inversely proportional to the concentration of antigen in a sample. We illustrate this method using the recombinant malaria antigen Plasmodium falciparum histidine-rich-protein 2 (rPfHRP2) spiked in human serum. This antigen was a recombinant HRP2 protein expressed in Escherichia coli, which is also the standard reference material. The limit of detection (LOD) of our immunoassay was found to be less than 6 ng mL-1 of rPfHRP2 within 20 min, which is approaching the desired sensitivity needed in the Target Product Profile (TPP) for malaria elimination settings. The concept presented here is flexible and may also be utilized for implementing fluorescence immunoassays for the parallel detection of biomarkers on capillary-driven microfluidic chips.

Comparison of ß-Amyloid Plaque Labeling Methods: Antibody Staining, Gallyas Silver Staining, and Thioflavin-S Staining.

Objective To evaluate senile plaque formation and compare the sensitivity of three different ß-amyloid (Aß) labeling methods (antibody staining, Gallyas silver staining, and thioflavin-S staining) to detect Aß deposition.Methods APPswe/PSEN1dE9 transgenic mice (APP/PS1) of different ages were used to examine spatiotemporal changes in Aß plaque deposition. Antibody staining, Gallyas silver staining, and thioflavin-S staining were used to detect Aß plaque deposition in the same brain region of adjacent slices from model mice, and the results were compared.Results With aging, Aß plaques first appeared in the cortex and then the deposition increased throughout the whole brain. Significantly greater plaque deposition was detected by 6E10 antibody than that analyzed with Gallyas silver staining or thioflavin-S staining (P<0.05). Plaque deposition did not show significant difference between the APP/PS1 mice brains assayed with Gallyas silver staining and ones with thioflavin-S staining (P=0.0033).Conclusions The APP/PS1 mouse model of Alzheimer's disease could mimick the progress of Aß plaques occurred in patients with Alzheimer's disease. Antibody detection of Aß deposition may be more sensitive than chemical staining methods.

Silver Staining Techniques of Polyacrylamide Gels.

After SDS-polyacrylamide gel electrophoresis the separated proteins have to be visualized by staining the gel. The same is true after transfer of separated proteins to a blotting membrane in order to verify an efficient transfer and to visualize the amount of protein(s) remaining in the gel. Several different staining techniques exist for staining of proteins in SDS-polyacrylamide gels. The sensitivity of these staining procedures are different, also the expenditure of time and other aspects. Still, silver staining is among the most sensitive and reliable staining technique. Because this technique was developed in the 1970s, a huge number of variations exist. Here, we will provide three variations, which are robust and easy to perform.

Principle and Method of Silver Staining of Proteins Separated by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis.

Silver staining is an excellent technique for detecting proteins which are separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis due to its efficiency of detecting proteins present in nanograms. The technique is based on the simple principle that selective reduction of silver into metallic silver occurs at the initiation site in the close proximity of protein molecules. The staining process sequentially consists of protein fixation, sensitization, washing, silver impregnation, and finally development of image. Depending upon the amount of silver incorporated into the protein bands, different color of gel is produced on silver staining. Though different protocols of silver staining exist, the method described here is easy, cheap, reliable, and very sensitive.

High-resolution synchrotron-based X-ray microtomography as a tool to unveil the three-dimensional neuronal architecture of the brain.

The assessment of neuronal number, spatial organization and connectivity is fundamental for a complete understanding of brain function. However, the evaluation of the three-dimensional (3D) brain cytoarchitecture at cellular resolution persists as a great challenge in the field of neuroscience. In this context, X-ray microtomography has shown to be a valuable non-destructive tool for imaging a broad range of samples, from dense materials to soft biological specimens, arisen as a new method for deciphering the cytoarchitecture and connectivity of the brain. In this work we present a method for imaging whole neurons in the brain, combining synchrotron-based X-ray microtomography with the Golgi-Cox mercury-based impregnation protocol. In contrast to optical 3D techniques, the approach shown here does neither require tissue slicing or clearing, and allows the investigation of several cells within a 3D region of the brain.

A Fast Silver Staining Protocol Enabling Simple and Efficient Detection of SSR Markers using a Non-denaturing Polyacrylamide Gel.

Simple Sequence Repeat (SSR) is one of the most effective markers used in plant and animal genetic research and molecular breeding programs. Silver staining is a widely used method for the detection of SSR markers in a polyacrylamide gel. However, conventional protocols for silver staining are technically demanding and time-consuming. Like many other biological laboratory techniques, silver staining protocols have been steadily optimized to improve detection efficiency. Here, we report a simplified silver staining method that significantly reduces reagent costs and enhances the detection resolution and picture clarity. The new method requires two major steps (impregnation and development) and three reagents (silver nitrate, sodium hydroxide, and formaldehyde), and only 7 min of processing for a non-denaturing polyacrylamide gel. Compared to previously reported protocols, this new method is easier, quicker and uses fewer chemical reagents for SSR detection. Therefore, this simple, low-cost, and effective silver staining protocol will benefit genetic mapping and marker-assisted breeding by a quick generation of SSR marker data.