Quantifying morphologies of developing neuronal cells using deep learning with imperfect annotations

The functionality of human intelligence relies on the interaction and health of neurons, hence, quantifying neuronal morphologies can be crucial for investigating the functionality of the human brain. This paper proposes a deep learning (DL) based method for segmenting and quantifying neuronal structures in fluorescence microscopy images of developing neuronal cells cultured in vitro. Compared to the majority of supervised DL-based segmentation methods that heavily rely on creating exact corresponding masks of neuronal structures for the preparation of training samples, the proposed approach allows for imperfect annotation of neurons, as it only requires tracing the centrelines of the neurites. This ability accelerates the preparation of training data by several folds. Our proposed framework is built on a modified version of PSPNet with an EfficientNet backbone pre-trained on the CityScapes dataset. To handle the imperfectness of training samples, we incorporated a weighted combination of two loss functions, namely the Dice loss and Lovász loss functions, into our network. We evaluated the proposed framework and several other state-of-the-art methods on a published dataset of approximately 900 manually quantified cultured mouse neurons. Our results indicate a close correlation between the proposed method and manual quantification in terms of neuron length and the number of branches while demonstrating improved analysis speed. Furthermore, the proposed method achieved high accuracy in neuron segmentation, as evidenced by the evaluation of the neurons' length and number of branches.

A critical role for Pol II CTD phosphorylation in heterochromatic gene activation

How gene activation works in heterochromatin, and how the mechanism might differ from the one used in euchromatin, has been largely unexplored. Previous work has shown that in SIR-regulated heterochromatin of Saccharomyces cerevisiae, gene activation occurs in the absence of covalent histone modifications and other alterations of chromatin commonly associated with transcription.Here we demonstrate that such activation occurs in a substantial fraction of cells, consistent with frequent transcriptional bursting, and this raises the possibility that an alternative activation pathway might be used. We address one such possibility, Pol II CTD phosphorylation, and explore this idea using a natural telomere-linked gene, YFR057w, as a model. Unlike covalent histone modifications, we find that Ser2, Ser5 and Ser7 CTD phosphorylated Pol II is prevalent at the drug-induced heterochromatic gene. Particularly enriched relative to the euchromatic state is Ser2 phosphorylation. Consistent with a functional role for Ser2P, YFR057w is negligibly activated in cells deficient in the Ser2 CTD kinases Ctk1 and Bur1 even though the gene is strongly stimulated when it is placed in a euchromatic context. Collectively, our results are consistent with a critical role for Ser2 CTD phosphorylation in driving Pol II recruitment and transcription of a natural heterochromatic gene - an activity that may supplant the need for histone epigenetic modifications.

A pH-Sensitive Double Chromophore Fluorescent Dye for Live-Tracking of Lipophagy

Lipid droplet (LD) degradation provides metabolic energy and important building blocks for various cellular processes. The two major LD degradation pathways include autophagy (lipophagy), which involves delivery of LDs to autolysosomes, and lipolysis, which is mediated by lipases. While abnormalities in LD degradation are associated with various pathological disorders, our understanding of lipophagy is still rudimentary. In this study, we describe the development of a lipophilic dye containing two fluorophores, one of which is pH-sensitive and the other pH-stable. We further demonstrate that this "Lipo-Fluddy" can be used to visualize and quantify lipophagy in living cells, in an easily applicable and protein label-free approach. After estimating the ability of compound candidates to penetrate LDs, we synthesized several BODIPY and (pH-switchable) rhodol dyes, whose fluorescence properties (incl. their photophysical compatibility) were analyzed. Of three Lipo-Fluddy dyes synthesized, one exhibited the desired properties and allowed observation of lipophagy by fluorescence microscopy. Also, this dye proved to be non-toxic and suitable for the examination of various cell lines. Moreover, a method was developed to quantify the lipophagy process using flow cytometry, which could be applied in the future in the identification of lipophagy-related genes or in the screening of potential drugs against lipophagy-related diseases.

When Weak Is Strong: A Plea for Low-Affinity Binders for Optical Microscopy

The exploitation of low-affinity molecular interactions in protein labeling is an emerging topic in optical microscopy. Such non-covalent and low-affinity interactions can be realized with various concepts from chemistry and for different molecule classes, and lead to a constant renewal of fluorescence signals at target sites. Further benefits are a versatile use across microscopy methods, in 3D, live and many-target applications. In recent years, several classes of low-affinity labels were developed and a variety of powerful applications demonstrated. Still, this research field is underdeveloped, while the potential is huge.

Detection and Quantification of Nanoparticle-Induced Intracellular ROS in Live Cells by Laser Scanning Confocal Microscopy

All living organisms utilise reactive oxygen species (ROS) for essential cellular functions, the majority of which involve signal transduction pathways, such as enzyme regulation, cell growth and differentiation signalling, and inflammation mediation. Increased ROS in cancer cells can be caused by abnormalities in the tumor environment. However, using fluorescence microscopy to detect and quantify ROS changes in biological systems is difficult for several reasons: (1) lack of specificity of ROS-sensitive probes, (2) high turnover of ROS species, (3) rapid decrease in ROS fluorescence with time, and (4) detection and quantification techniques with insufficient sensitivity. Existing approaches to ROS measurement using confocal microscopy imaging focus solely on ROS detection rather than quantification. A novel fluorescence-based ROS detection and quantification technique has been developed for the purpose of resolving the limitations of existing methods. In general, ROS is detected by fluorescence using instrumentation such as flow cytometry and laser scanning confocal microscopy. However, these approaches confirm only the presence or absence of ROS; they are not quantitative, which is essential for therapeutic applications. In the newly developed technique, cerium-based ROS-generating nanoparticles have been used to elevate the ROS in HT-1080 fibrosarcoma cells. The elevated ROS levels are detected using an H2DCFDA fluorescence probe, which is used widely for this application, and captured as digital images using a 488 nm fluorescence channel. Quantification of the ROS is achieved using script in MATLAB software to convert the fluorescence intensities to numerical values. Thus, this technique nearly simultaneously integrates both detection and quantification of the ROS, which provides the statistical justification necessary to support therapeutic translation.

Fluorescence fluctuation based super resolution microscopy, basic concepts for an easy start

Due to the wave nature of light, optical microscopy has a lower-bound lateral resolution limit of approximately half of the wavelength of visible light, i.e., within the range of 200 to 350 nm. Fluorescence Fluctuation based Super Resolution Microscopy (FF-SRM) is a term used to encompass a collection of image analysis techniques which rely on the statistical processing of temporal variations of the fluorescence signal. FF-SRM aims to reduce the uncertainty of the location of fluorophores within an image, often improving spatial resolution to several tens of nanometers. FF-SRM is suitable for live-cell imaging due to its compatibility with most fluorescent probes and relatively simple instrumental and experimental requirements, which are mostly camera-based epifluorescence instruments. Each FF-SRM approach has strengths and weaknesses, which depend directly on the underlying statistical principles through which enhanced spatial resolution is achieved. In this review, the basic concepts and principles behind a range of FF-SRM methods published to date are described. Their operational parameters are explained and guidance for its selection is provided. This article is protected by copyright. All rights reserved.

ContactJ: Characterization of lipid droplet-mitochondrial contacts using fluorescence microscopy and image analysis

Lipid droplets (LDs) are the major lipid storage organelles of eukaryotic cells and together with mitochondria key regulators of cell bioenergetics. LDs communicate with mitochondria and other organelles forming “metabolic synapse” contacts to ensure that lipid supply occurs where and when necessary. Although transmission electron microscopy analysis allows an accurate and precise analysis of contacts, the characterization of a large number of cells and conditions can become a long-term process. In order to extend contact analysis to hundreds of cells and multiple conditions, we have combined confocal fluorescence microscopy with advanced image analysis methods. In this work, we have developed the ImageJ macro script ContactJ, a novel and straight image analysis method to identify and quantify contacts between LD and mitochondria in fluorescence microscopy images allowing the automatic analysis. This image analysis workflow combines colocalization and skeletonization methods, enabling the quantification of LD-mitochondria contacts together with a complete characterization of organelles and cellular parameters. The correlation and normalization of these parameters contribute to the complex description of cell behavior under different experimental energetic states. ContactJ is available here: https://doi.org/10.5281/zenodo.5810874

Structural Properties Dictating Selective Optotracer Detection of S. aureus

Optotracers are conformation‐sensitive fluorescent tracer molecules that detect peptide‐ and carbohydrate‐based biopolymers. Their binding to bacterial cell walls allows selective detection and visualisation of Staphylococcus aureus (S. aureus). Here, we investigated the structural properties providing optimal detection of S. aureus. We quantified spectral shifts and fluorescence intensity in mixes of bacteria and optotracers, using automatic peak analysis, cross‐correlation, and area‐under‐curve analysis. We found that the length of the conjugated backbone and the number of charged groups, but not their distribution, are important factors for selective detection of S. aureus. The photophysical properties of optotracers were greatly improved by incorporating a donor‐acceptor‐donor (D‐A‐D)‐type motif in the conjugated backbone. With significantly reduced background and binding‐induced on‐switch of fluorescence, these optotracers enabled real‐time recordings of S. aureus growth. Collectively, this demonstrates that chemical structure and photophysics are key tunable characteristics in the development of optotracers for selective detection of bacterial species.

Carbonate-Based Fluorescent Chemical Tool for Uncovering Carboxylesterase 1 (CES1) Activity Variations in Live Cells

Carboxylesterase 1 (CES1) plays a key role in the metabolism of endogenous biomolecules and xenobiotics including a variety of pharmaceuticals. Despite the established importance of CES1 in drug metabolism, methods to study factors that can vary CES1 activity are limited with only a few suitable for use in live cells. Herein, we report the development of FCP1, a new CES1 specific fluorescent probe with a unique carbonate substrate constructed from commercially available reagents. We show that FCP-1 can specifically report on endogenous CES1 activity with a robust fluorescence response in live HepG2 cells through studies with inhibitors and genetic knockdowns. Subsequently, we deployed FCP-1 to develop a live cell fluorescence microscopy-based approach to identify activity differences between CES1 isoforms. To the best of our knowledge, this is the first application of a fluorescent probe to measure the activity of CES1 sequence variants in live cells.

Enhanced fluorescence from semiconductor quantum dot-labelled cells excited at 280 nm

Semiconductor quantum dots (QDs) have significant advantages over more traditional fluorophores used in fluorescence microscopy including reduced photobleaching, long-term photostability and high quantum yields, but due to limitations in light sources and optics, are often excited far from their optimum excitation wavelengths in the deep-UV. Here, we present a quantitative comparison of the excitation of semiconductor QDs at a wavelength of 280 nm, compared to the longer wavelength of 365 nm, within a cellular environment. We report increased fluorescence intensity and enhanced image quality when using 280 nm excitation compared to 365 nm excitation for cell imaging across multiple datasets, with a highest average fluorescence intensity increase of 3.59-fold. We also find no significant photobleaching of QDs associated with 280 nm excitation and find that on average, ~80% of cells can tolerate exposure to high-intensity 280 nm irradiation over a 6-hour period.

Deconvolution Microscopy: A Platform for Rapid On-Site Evaluation (ROSE) of Fine Needle Aspiration (FNA) Specimens that Enables Recovery of the Sample

CONTEXT

Rapid on-site evaluation (ROSE) optimizes the performance of cytology, but requires skilled handling, and smearing can make the material unavailable for some ancillary tests. There is a need to facilitate ROSE without sacrificing part of the sample.

OBJECTIVE

We evaluated the image quality of inexpensive deconvolution fluorescence microscopy for optically sectioning non-smeared FNA tissue fragments.

DESIGN

A portion of residual material from 14 FNA samples was stained for 3 minutes in Hoechst 33342 and Sypro^TM Red to label DNA and protein respectively, transferred to an imaging chamber, and imaged at 200X or 400X magnification at 1 micron intervals using a GE DeltaVision inverted fluorescence microscope. A deconvolution algorithm was applied to remove out of plane signal, and resulting images were inverted and pseudocolored to resemble an H&E section. Five cytopathologists blindly diagnosed 2 to 4 representative image stacks per case (total 70 evaluations), and later compared them to conventional epifluorescent images.

RESULTS

Accurate definitive diagnoses were rendered in 45 of 70 (64%) total evaluations; equivocal diagnoses (atypical or suspicious) were made in 21 of 70 (30%). There were two false positive and two false negative "definite" diagnoses in three cases (4/70; 6%). Cytopathologists preferred deconvolved images compared to raw images (p< 0.01). The imaged fragments were recovered and prepared into a ThinPrep or cell block without discernable alteration.

CONCLUSIONS

Deconvolution improves image quality of FNA fragments compared to epifluorescence, often allowing definitive diagnosis while enabling the ROSE material to be subsequently triaged.

Imaging Mitosis with Lattice LightSheet

Mitosis is one of the most fundamental processes of life, allowing organisms to grow, develop, and evolve. Acquiring microscopic images and understanding the detailed mechanism of this process is critical in the fields of cell and developmental biology. Modern fluorescence microscopy is the standard for imaging specific molecules and proteins as they interact during this complicated process. However, researchers must take care to ensure that they are maintaining the basal cell processes during mitosis without disruption by placing the sample on a microscope. In addition, mitosis in itself is an incredibly dynamic process that requires both high-speed and high-resolution imaging (McIntosh and Hays. Biology. 5:55, 2016). The Lattice LightSheet is an advanced system, developed in the lab of Eric Betzig (Chen et al. Science. 346:1257998), that offers imaging speeds in the volumes/second while still resolving fine, intracellular structures. Here we describe how to prepare cell culture samples for ideal mitotic imaging on this cutting-edge light sheet fluorescence microscope.

Multi-dimensional Fluorescence Live-Cell Imaging for Glucosome Dynamics in Living Human Cells

Fluorescence live-cell imaging that has contributed to our understanding of cell biology is now at the frontline of studying quantitative biochemistry in a cell. Particularly, technological advancements of fluorescence live-cell imaging and associated strategies in recent years have allowed us to discover various subcellular macromolecular assemblies in living human cells. Here we describe how real-time dynamics of a multienzyme metabolic assembly, the "glucosome," that is responsible for regulating glucose flux at subcellular levels, has been investigated in both 2- and 3-dimensional space of single human cells. We envision that such multi-dimensional fluorescence live-cell imaging will continue to revolutionize our understanding of how intracellular metabolic pathways and their network are functionally orchestrated at single-cell levels.

High-resolution 3D mapping of rhizosphere glycan patterning using molecular probes in a transparent soil system

Rhizospheres are microecological zones at the interface of roots and soils. Interactions between bacteria and roots are critical for maintaining plant and soil health but are difficult to study because of constraints inherent in working with underground systems. We have developed an in-situ rhizosphere imaging system based on transparent soils and molecular probes that can be imaged using confocal microscopy. We observed spatial patterning of polysaccharides along roots and on cells deposited into the rhizosphere and also co-localised fluorescently tagged soil bacteria. These studies provide insight into the complex glycan landscape of rhizospheres and suggest a means by which root / rhizobacteria interactions can be non-disruptively studied.

HSP90 inhibitors reduce cholesterol storage in Niemann-Pick type C1 mutant fibroblasts

Niemann-Pick type C1 (NPC1) disease is a lysosomal lipid storage disorder caused by mutations of the NPC1 gene. More than 300 disease-associated mutations are reported in patients, resulting in abnormal accumulation of unesterified cholesterol, glycosphingolipids, and other lipids in late endosomes and lysosomes (LE/Ly) of many cell types. Previously, we showed that treatment of many different NPC1 mutant fibroblasts with histone deacetylase inhibitors resulted in reduction of cholesterol storage, and we found that this was associated with enhanced exit of the NPC1 protein from the endoplasmic reticulum and delivery to LE/Ly. This suggested that histone deacetylase inhibitors may work through changes in protein chaperones to enhance the folding of NPC1 mutants, allowing them to be delivered to LE/Ly. In this study, we evaluated the effect of several HSP90 inhibitors on NPC1^I1061T skin fibroblasts. We found that HSP90 inhibition resulted in clearance of cholesterol from LE/Ly, and this was associated with enhanced delivery of the mutant NPC1^I1061T protein to LE/Ly. We also observed that inhibition of HSP90 increased the expression of HSP70, and overexpression of HSP70 also reduced cholesterol storage in NPC1^I1061T fibroblasts. However, we did not see correction of cholesterol storage by arimoclomol, a drug that is reported to increase HSP70 expression, at doses up to 0.5 mM. The increase in other chaperones as a consequence of HSP90 improves folding of NPC1 protein and relieves cholesterol accumulation in NPC1 mutant fibroblasts.

The use of fluorescence lifetime technology in benign and malignant thyroid tissues

OBJECTIVE

To explore the use of fluorescence lifetime imaging microscopy in thyroid tissues, and to investigate how different thyroid lesions affect fluorescence lifetime.

METHOD

Fluorescence lifetime measurements were taken of fresh frozen thyroid surgical specimens stained with fluorescein isothiocyanate tagged anti-thyroglobulin monoclonal antibodies.

RESULTS

The mean fluorescence lifetime measurements in 12 patients - 3 with multinodular goitre, 4 with follicular adenoma, 4 with papillary thyroid carcinoma and 1 with follicular carcinoma - were 3.16 ns (range, 2.66-3.52 ns), 3.75 ns (range, 2.99-4.57 ns), 2.97 ns (range, 2.57-3.21 ns) and 3.61 ns, respectively. The fluorescence lifetime of follicular adenoma patients was higher than that of papillary thyroid carcinoma patients by 26 per cent (p = 0.058). The fluorescence lifetime in the follicular carcinoma patient was similar to the follicular adenoma group, but higher than in the papillary thyroid carcinoma group by 22 per cent (p = 0.01).

CONCLUSION

Fluorescence lifetime measurements varied in different thyroid pathologies, possibly because of tissue-scale structural influences.

Capturing Single-Cell Phenotypic Variation via Unsupervised Representation Learning

We propose a novel variational autoencoder (VAE) framework for learning representations of cell images for the domain of image-based profiling, important for new therapeutic discovery. Previously, generative adversarial network-based (GAN) approaches were proposed to enable biologists to visualize structural variations in cells that drive differences in populations. However, while the images were realistic, they did not provide direct reconstructions from representations, and their performance in downstream analysis was poor. We address these limitations in our approach by adding an adversarial-driven similarity constraint applied to the standard VAE framework, and a progressive training procedure that allows higher quality reconstructions than standard VAE's. The proposed models improve classification accuracy by 22% (to 90%) compared to the best reported GAN model, making it competitive with other models that have higher quality representations, but lack the ability to synthesize images. This provides researchers a new tool to match cellular phenotypes effectively, and also to gain better insight into cellular structure variations that are driving differences between populations of cells.

Fluorescence Microscopy Imaging Calibration for Quantifying Nanocarrier Binding to Cells During Shear Flow Exposure

Targeted drug delivery is a fast growing industry in healthcare and technologies are being developed for applications utilizing nanocarriers as vehicles for drug transport. As the size scale of these particles becomes further reduced, advanced fluorescence microscopy and image analysis techniques become increasingly important for facilitating our understanding of nanocarrier binding and avidity, thereby establishing the basis for nanocarrier design optimization. While there is a significant body of published work using nanocarriers in vitro and in vivo, the advent of smaller particles that have typically been studied (~500 nm) limits the ability to attain quantitative measurements of nanocarrier binding dynamics since image acquisition and analysis methods are restricted by microscopy pixel size. This work demonstrates the use of a novel calibration technique based on radioisotope counting and fluorescence imaging for enabling quantitative determination of nanocarrier binding dynamics. The technique is then applied to assess the temporal profile of endothelial cell binding of two antibody targeted nanocarrier types in the presence of fluid shear stress. Results are provided for binding of nanoparticles smaller than a microscopy image pixel.

Single particle tracking of ADAMTS13 (a disintegrin and metalloprotease with thrombospondin type-1 repeats) molecules on endothelial von Willebrand factor strings

von Willebrand factor (VWF) strings are removed from the endothelial surface by ADAMTS13 (a disintegrin and metalloprotease with thrombospondin type-1 repeats)-mediated proteolysis. To visualize how single ADAMTS13 molecules bind to these long strings, we built a customized single molecule fluorescence microscope and developed single particle tracking software. Extensive analysis of over 6,000 single inactive ADAMTS13(E225Q) enzymes demonstrated that 20% of these molecules could be detected in at least two consecutive 60-ms frames and followed two types of trajectories. ADAMTS13(E225Q) molecules either decelerated in the vicinity of VWF strings, whereas sometimes making brief contact with the VWF string before disappearing again, or readily bound to the VWF strings and this for 120 ms or longer. These interactions were observed at several sites along the strings. Control experiments using an IgG protein revealed that only the second type of trajectory reflected a specific interaction of ADAMTS13 with the VWF string. In conclusion, we developed a dedicated single molecule fluorescence microscope for detecting single ADAMTS13 molecules (nm scale) on their long, flow-stretched VWF substrates (μm scale) anchored on living cells. Comprehensive analysis of all detected enzymes showed a random interaction mechanism for ADAMTS13 with many available binding sites on the VWF strings.