Single-cell Fluorescence Imaging Research Articles

Leukocyte differential based on an imaging and impedance flow cytometry of microfluidics coupled with deep neural networks.

The differential of leukocytes functions as the first indicator in clinical examinations. However, microscopic examinations suffered from key limitations of low throughputs in classifying leukocytes while commercially available hematology analyzers failed to provide quantitative accuracies in leukocyte differentials. A home-developed imaging and impedance flow cytometry of microfluidics was used to capture fluorescent images and impedance variations of single cells traveling through constrictional microchannels. Convolutional and recurrent neural networks were adopted for data processing and feature extractions, which were then fused by a support vector machine to realize the four-part differential of leukocytes. The classification accuracies of the four-part leukocyte differential were quantified as 95.4% based on fluorescent images plus the convolutional neural network, 90.3% based on impedance variations plus the recurrent neural network, and 99.3% on the basis of fluorescent images, impedance variations, and deep neural networks. Based on single-cell fluorescent imaging and impedance variations coupled with deep neural networks, the four-part leukocyte differential can be realized with almost 100% accuracy.

Label-Free Single-Cell SERS Detection and Fluorescence Imaging of Molecular Responses to Endoplasmic Reticulum Stress under Electrical Stimulation.

The endoplasmic reticulum (ER) is one of the most important organelles in eukaryotic cells, in which most proteins and lipids are synthesized to regulate complex cellular processes. Generally, the excessive accumulation of unfolded or misfolded proteins can disturb ER homeostasis and induce endoplasmic reticulum stress (ERS). Howbeit, the molecular stress responses within ERS and metastatic behaviors of tumor cells during electrical stimulation (ES) are still poorly investigated and remain a challenge. In this study, by the combined use of fluorescence imaging, ER-targeting plasmonic nanoprobes were developed to trace molecular stress response profiling within the ER during a constant-voltage ES process at ∼1 V based on label-free surface-enhanced Raman spectroscopy (SERS). The excess accumulation of β-misfolded proteins was found after the ES, leading to breaking of the ER homeostasis and further inducing mitochondrial dysfunction. Notably, the excessive stress of ER under ES can destroy the calcium ion balance and induce significant upregulation of calreticulin expression. Importantly, the content ratio of two kinds of cadherin between E-cadherin and N-cadherin was gradually improved with the voltages boosted. Meanwhile, the epithelial adhesion factor expression was ascended with voltages amplified, leading to inhibiting tumor cell migration at low voltages or death under higher voltages (∼1 V). This study provides cellular insights into the ES approach for tumor therapy and also provides a simple and effective method for detecting molecular stress responses in endoplasmic reticulum stress.

L-Carnitine Suppresses Transient Receptor Potential Vanilloid Type 1 Activation in Human Corneal Epithelial Cells.

Tear film hyperosmolarity induces dry eye syndrome (DES) through transient receptor potential vanilloid type 1 (TRPV1) activation. L-carnitine is a viable therapeutic agent since it protects against this hypertonicity-induced response. Here, we investigated whether L-carnitine inhibits TRPV1 activation by blocking heat- or capsaicin-induced increases in Ca2+ influx or hyperosmotic stress-induced cell volume shrinkage in a human corneal epithelial cell line (HCE-T). Single-cell fluorescence imaging of calcein/AM-loaded cells or fura-2/AM-labeled cells was used to evaluate cell volume changes and intracellular calcium levels, respectively. Planar patch-clamp technique was used to measure whole-cell currents. TRPV1 activation via either capsaicin (20 µmol/L), hyperosmolarity (≈450 mosmol/L) or an increase in ambient bath temperature to 43 °C induced intracellular calcium transients and augmented whole-cell currents, whereas hypertonicity induced cell volume shrinkage. In contrast, either capsazepine (10 µmol/L) or L-carnitine (1-3 mmol/L) reduced all these responses. Taken together, L-carnitine and capsazepine suppress hypertonicity-induced TRPV1 activation by blocking cell volume shrinkage.

DeepIFC: Virtual fluorescent labeling of blood cells in imaging flow cytometry data with deep learning.

Imaging flow cytometry (IFC) combines flow cytometry with microscopy, allowing rapid characterization of cellular and molecular properties via high-throughput single-cell fluorescent imaging. However, fluorescent labeling is costly and time-consuming. We present a computational method called DeepIFC based on the Inception U-Net neural network architecture, able to generate fluorescent marker images and learn morphological features from IFC brightfield and darkfield images. Furthermore, the DeepIFC workflow identifies cell types from the generated fluorescent images and visualizes the single-cell features generated in a 2D space. We demonstrate that rarer cell types are predicted well when a balanced data set is used to train the model, and the model is able to recognize red blood cells not seen during model training as a distinct entity. In summary, DeepIFC allows accurate cell reconstruction, typing and recognition of unseen cell types from brightfield and darkfield images via virtual fluorescent labeling.

Development of a Repair Enzyme Fluorescent Probe to Reveal the Intracellular DNA Damage Induced by Benzo[a]pyrene in Living Cells

Pollutant exposure causes a series of DNA damage in cells, resulting in the initiation and progression of diseases and even cancers. An investigation of the DNA damage induced by pollutants in living cells is significant to evaluate the cytotoxicity, genotoxicity, and carcinogenicity of environmental exposure, providing critical insight in the exploration of the etiologies of diseases. In this study, we develop a repair enzyme fluorescent probe to reveal the DNA damage caused by an environmental pollutant in living cells by single-cell fluorescent imaging of the most common base damage repair enzyme named human apurinic/apyrimidinic endonuclease 1 (APE1). The repair enzyme fluorescent probe is fabricated by conjugation of an APE1 high affinity DNA substrate on a ZnO2 nanoparticle surface to form a ZnO2@DNA nanoprobe. The ZnO2 nanoparticle serves as both a probe carrier and a cofactor supplier, releasing Zn2+ to activate APE1 generated by pollutant exposure. The AP-site in the DNA substrate of the fluorescent probe is cleaved by the activated APE1, releasing fluorophore and generating fluorescent signals to indicate the position and degree of APE1-related DNA base damage in living cells. Subsequently, the developed ZnO2@DNA fluorescent probe is applied to investigate the APE1-related DNA base damage induced by benzo[a]pyrene (BaP) in living human hepatocytes. Significant DNA base damage by BaP exposure is revealed, with a positive correlation of the damage degree with exposure time in 2-24 h and the concentration in 5-150 μM, respectively. The experimental results demonstrate that BaP has a significant effect on the AP-site damage, and the degree of DNA base damage is time-dependent and concentration-dependent.

Gold Ions Hyperpolarize Bacteria

Background: The study of bacterial electrophysiology is important for understanding antibacterial resistance, biofilm formation, and fundamental questions of cell growth and division. These experiments require new tools to modulate the resting membrane potential of bacteria. The use of potassium and magnesium ions, antibiotics, short exposures to blue light, and electric field have been used to hyperpolarize or depolarize bacteria. Our research characterizes the cellular response to a new reagent, gold ions, using single-cell imaging. Methods: We use fluorescence microscopy to monitor, in real time, the change to the membrane potential when Bacillus subtilis (B. subtilis) and Escherichia coli (E. coli) are exposed to gold ions. Membrane potential is measured with two different Nernstian dyes, thioflavin T and tetramethylrhodamine methyl ester. Gold ions are introduced to cell by adding gold salt solutions or through the electrochemical generation of gold ions. Inductively coupled plasma mass spectrometry (ICP-MS) is used to determine the concentration of gold ions generated electrochemically. Standard growth curves are used to study the effect of gold ions on bacterial growth. Results: Single cell fluorescence imaging shows that a solution of gold ions hyperpolarizes B. subtilis and E. coli in a concentration-dependent manner. ICP-MS confirms that applied voltage and frequency controls the concentration of gold ions generated electrochemically. Electrochemically generated gold ions diffuse through the imaging chamber creating a wave of hyperpolarization. The speed of the hyperpolarization wave can be modulated by voltage and frequency. Conclusions: Our research describes a new tool, gold ions, for the hyperpolarization of bacteria. Gold ions can be introduced to bacteria as a salt solution or generated electrochemically, providing spatial and temporal control of bacterial membrane potential. Beyond this work, it is possible that hyperpolarization may play a role in the use of gold as an antibacterial agent.

Real-Time Fluorescence Microscopy on Living E. coli Sheds New Light on the Antibacterial Effects of the King Penguin β-Defensin AvBD103b.

(1) Antimicrobial peptides (AMPs) are a promising alternative to conventional antibiotics. Among AMPs, the disulfide-rich β-defensin AvBD103b, whose antibacterial activities are not inhibited by salts contrary to most other β-defensins, is particularly appealing. Information about the mechanisms of action is mandatory for the development and approval of new drugs. However, data for non-membrane-disruptive AMPs such as β-defensins are scarce, thus they still remain poorly understood. (2) We used single-cell fluorescence imaging to monitor the effects of a β-defensin (namely AvBD103b) in real time, on living E. coli, and at the physiological concentration of salts. (3) We obtained key parameters to dissect the mechanism of action. The cascade of events, inferred from our precise timing of membrane permeabilization effects, associated with the timing of bacterial growth arrest, differs significantly from the other antimicrobial compounds that we previously studied in the same physiological conditions. Moreover, the AvBD103b mechanism does not involve significant stereo-selective interaction with any chiral partner, at any step of the process. (4) The results are consistent with the suggestion that after penetrating the outer membrane and the cytoplasmic membrane, AvBD103b interacts non-specifically with a variety of polyanionic targets, leading indirectly to cell death.

Min Oscillations as Real-time Reporter of Sublethal Effects in Photodynamic Treatment of Bacteria.

The Min protein system is a cell division regulator in Escherichia coli. Under normal growth conditions, MinD is associated with the membrane and undergoes pole-to-pole oscillations. The period of these oscillations has been previously proposed as a reporter for the bacterial physiological state at the single-cell level and has been used to monitor the response to sublethal challenges from antibiotics, temperature, or mechanical fatigue. Using real-time single-cell fluorescence imaging, we explore here the effect of photodynamic treatment on MinD oscillations. Irradiation of bacteria in the presence of the photosensitizer methylene blue disrupts the MinD oscillation pattern depending on its concentration. In contrast to antibiotics, which slow down the oscillation, photodynamic treatment results in an abrupt interruption, reflecting divergent physiological mechanisms leading to bacterial death. We show that MinD oscillations are sensitive to mild photodynamic effects that are overlooked by traditional methods, expanding the toolbox for mechanistic studies in antimicrobial photodynamic therapy.

Abstract 10691: Single Cell Florescence Imaging in Hypertrophic Cardiomyopathy Reveals a Proarrhythmic Substrate: Implications for Arrhythmogenesis and Antiarrhythmic Therapy

Introduction: Hypertrophic cardiomyopathy (HCM) is associated with high morbidity and mortality and remains the leading cause of sudden death in young people. Despite 5 decades of research, there is no disease modifying therapy for HCM. The cellular mechanisms leading to a proarrhythmic substrate are not yet fully elucidated but may be patient-specific. Here, we present single cell electrophysiology results of adult cardiomyocytes isolated from a cohort of HCM patients who underwent septal reduction therapy with surgical myectomy. Methods: Freshly isolated surgical specimens from HCM patients were enzymatically digested into single ventricular myocytes and compared to discarded wild-type (WT) donor hearts as controls. Myocytes displayed characteristic rod-shaped morphology, clear sarcolemmal ultrastructure, and intact plasma membranes without significant inclusions. After Ca 2+ readaptation and labeling with both a voltage and Ca 2+ sensitive fluorescent dye, cells were field stimulated at various pacing frequencies to obtain voltage and Ca 2+ tracings. APD restitution, response to drug therapy, and baseline data was compared to patient’s clinical data including electrocardiography, pathology, and multimodality imaging. Results: As compared to WT controls, HCM myocytes displayed significantly prolonged APD and Ca 2+ transients, as well as steeper APD restitution at all pacing frequencies tested. These results correlated with clinical QTc prolongation which was evident in HCM patients’ baseline ECGs that was not seen in controls. Despite genetic diversity in HCM samples, the HCM specimens appeared to share a common proarrhythmic phenotype. Finally, pathologic analysis of the myectomy specimens revealed evidence of myocyte hypertrophy, fibrosis, and cellular disarray, consistent with the clinical diagnosis of HCM. Conclusions: The single cell electrophysiology of HCM is markedly different than WT controls and displays a proarrhythmic phenotype. Single cell fluorescence imaging of a patient’s myocytes is a promising approach to elucidate patient specific electrophysiologic signatures and predict precision therapies for these patients.

In Situ Formation of Au-Glycopolymer Nanoparticles for Surface-Enhanced Raman Scattering-Based Biosensing and Single-Cell Immunity.

Successful synthesis of glyconanoparticles has attracted much attention due to their various biointeractive capabilities, but it is still a challenge to understand different single-cell responses to exogenous particles among cell populations. Herein, we designed polyaniline-containing galactosylated gold nanoparticles (Au@PGlyco NPs) via in situ polymerization of ortho-nitrophenyl-β-galactoside assisted by Au nucleation. The nanogold-carrying polyaniline block produced electromagnetic enhancement in surface-enhanced Raman scattering (SERS). The underlying polymerization mechanism of ortho-nitrophenyl compounds via the formation of Au nanoparticles was investigated. Depending on how the galactoside moiety reacted with β-galactosidase derived from bacteria, the Au@PGlyco NPs-mediated SERS biosensor could detect low amounts of bacteria (∼1 × 102 CFU/mL). In addition, a high accumulation of Au@PGlyco NPs mediated the immune response of tumor-associated M2 macrophages to the immunogenic M1 macrophage transition, which was elicited by reactive oxygen levels biostimulation using single-cell SERS-combined fluorescence imaging. Our study suggested that Au@PGlyco NPs may serve as a biosensing platform with the labeling capacity on galactose-binding receptors expressed cell and immune regulation.

Quantification of Interbacterial Competition using Single-Cell Fluorescence Imaging

Interbacterial competition can directly impact the structure and function of microbiomes. This work describes a fluorescence microscopy approach that can be used to visualize and quantify competitive interactions between different bacterial strains at the single-cell level. The protocol described here provides methods for advanced approaches in slide preparation on both upright and inverted epifluorescence microscopes, live-cell and time-lapse imaging techniques, and quantitative image analysis using the open-source software FIJI. The approach in this manuscript outlines the quantification of competitive interactions between symbiotic Vibrio fischeri populations by measuring the change in area over time for two coincubated strains that are expressing different fluorescent proteins from stable plasmids. Alternative methods are described for optimizing this protocol in bacterial model systems that require different growth conditions. Although the assay described here uses conditions optimized for V. fischeri, this approach is highly reproducible and can easily be adapted to study competition among culturable isolates from diverse microbiomes.

Quantification of Interbacterial Competition using Single-Cell Fluorescence Imaging

Interbacterial competition can directly impact the structure and function of microbiomes. This work describes a fluorescence microscopy approach that can be used to visualize and quantify competitive interactions between different bacterial strains at the single-cell level. The protocol described here provides methods for advanced approaches in slide preparation on both upright and inverted epifluorescence microscopes, live-cell and time-lapse imaging techniques, and quantitative image analysis using the open-source software FIJI. The approach in this manuscript outlines the quantification of competitive interactions between symbiotic Vibrio fischeri populations by measuring the change in area over time for two coincubated strains that are expressing different fluorescent proteins from stable plasmids. Alternative methods are described for optimizing this protocol in bacterial model systems that require different growth conditions. Although the assay described here uses conditions optimized for V. fischeri, this approach is highly reproducible and can easily be adapted to study competition among culturable isolates from diverse microbiomes.

Multimodal FACED imaging for large-scale single-cell morphological profiling

Free-space angular-chirp-enhanced delay (FACED) is an ultrafast laser-scanning technique that allows for high imaging speed at the scale orders of magnitude greater than the current technologies. However, this speed advantage has only been restricted to bright-field and fluorescence imaging—limiting the variety of image contents and hindering its applicability in image-based bioassay, which increasingly demands rich phenotypic readout at a large scale. Here, we present a new high-speed quantitative phase imaging (QPI) based on time-interleaved phase-gradient FACED image detection. We further integrate this system with a microfluidic flow cytometer platform that enables synchronized and co-registered single-cell QPI and fluorescence imaging at an imaging throughput of 77 000 cells/s with sub-cellular resolution. Combined with deep learning, this platform empowers comprehensive image-based profiling of single-cell biophysical phenotypes that can offer not only sufficient label-free power for cell-type classification but also cell-cycle phase tracking with high accuracy comparable to the gold-standard fluorescence method. This platform further enables correlative, compartment-specific single-cell analysis of the spatially resolved biophysical profiles at the throughput inaccessible with existing QPI methods. The high imaging throughput and content given by this multimodal FACED imaging system could open new opportunities in image-based single-cell analysis, especially systematic analysis that correlates the biophysical and biochemical information of cells, and provide new mechanistic insights into biophysical heterogeneities in many biological processes.

Manganese dioxide nanosheets induce mitochondrial toxicity in fish gill epithelial cells

The development and production of engineered 2D nanomaterials are expanding exponentially, increasing the risk of their release into the aquatic environment. A recent study showed 2D MnO2 nanosheets, under development for energy and biomedical applications, dissolve upon interaction with biological reducing agents, resulting in depletion of intracellular glutathione levels within fish gill cells. However, little is known concerning their toxicity and interactions with subcellular organelles. To address this gap, we examined cellular uptake, cytotoxicity and mitochondrial effects of 2D MnO2 nanosheets using an in vitro fish gill cell line to represent a target tissue of rainbow trout, a freshwater indicator species. The data demonstrate cellular uptake of MnO2 nanosheets into lysosomes and potential mechanisms of dissolution within the lysosomal compartment. MnO2 nanosheets induced severe mitochondrial dysfunction at sub-cytotoxic doses. Quantitative, single cell fluorescent imaging revealed mitochondrial fission and impaired mitochondrial membrane potential following MnO2 nanosheet exposure. Seahorse analyses for cellular respiration revealed that MnO2 nanosheets inhibited basal respiration, maximal respiration and the spare respiratory capacity of gill cells, indicating mitochondrial dysfunction and reduced cellular respiratory activity. MnO2 nanosheet exposure also inhibited ATP production, further supporting the suppression of mitochondrial function and cellular respiration. Together, these observations indicate that 2D MnO2 nanosheets impair the ability of gill cells to respond to energy demands or prolonged stress. Finally, our data demonstrate significant differences in the toxicity of the 2D MnO2 nanosheets and their microparticle counterparts. This exemplifies the importance of considering the unique physical characteristics of 2D nanomaterials when conducting safety assessments.

PN-ImTLSM facilitates high-throughput low background single-molecule localization microscopy deep in the cell.

When imaging the nucleus structure of a cell, the out-of-focus fluorescence acts as background and hinders the detection of weak signals. Light-sheet fluorescence microscopy (LSFM) is a wide-field imaging approach which has the best of both background removal and imaging speed. However, the commonly adopted orthogonal excitation/detection scheme is hard to be applied to single-cell imaging due to steric hindrance. For LSFMs capable of high spatiotemporal single-cell imaging, the complex instrument design and operation largely limit their throughput of data collection. Here, we propose an approach for high-throughput background-free fluorescence imaging of single cells facilitated by the Immersion Tilted Light Sheet Microscopy (ImTLSM). ImTLSM is based on a light-sheet projected off the optical axis of a water immersion objective. With the illumination objective and the detection objective placed opposingly, ImTLSM can rapidly patrol and optically section multiple individual cells while maintaining single-molecule detection sensitivity and resolution. Further, the simplicity and robustness of ImTLSM in operation and maintenance enables high-throughput image collection to establish background removal datasets for deep learning. Using a deep learning model to train the mapping from epi-illumination images to ImTLSM illumination images, namely PN-ImTLSM, we demonstrated cross-modality fluorescence imaging, transforming the epi-illumination image to approach the background removal performance obtained with ImTLSM. We demonstrated that PN-ImTLSM can be generalized to large-field homogeneous illumination imaging, thereby further improving the imaging throughput. In addition, compared to commonly used background removal methods, PN-ImTLSM showed much better performance for areas where the background intensity changes sharply in space, facilitating high-density single-molecule localization microscopy. In summary, PN-ImTLSM paves the way for background-free fluorescence imaging on ordinary inverted microscopes.

Quantification of interbacterial competition using single-cell fluorescence imaging

Quantification of interbacterial competition using single-cell fluorescence imaging

Preparation, Administration, and Assessment of In vivo Tissue-Specific Cellular Uptake of Fluorescent Dye-Labeled Liposomes.

There is a growing interest in using liposomes to deliver compounds in vivo particularly for targeted treatment approaches. Depending on the liposome formulation, liposomes may be preferentially taken up by different cell types in the body. This may influence the efficacy of the therapeutic particle as progression of different diseases is tissue- and cell-type-specific. In this protocol, we present one method for synthesizing and fluorescently labeling liposomes using DSPC, cholesterol, and PEG-2000 DSPE and the lipid dye DiD as a fluorescent label. This protocol also presents an approach for delivering liposomes in vivo and assessing cell-specific uptake of liposomes using flow cytometry. This approach can be used to determine the types of cells that take up liposomes and quantify the distribution and proportion of liposome-uptake across cell types and tissues. While not mentioned in this protocol, additional assays such as immunofluorescence and single-cell fluorescence imaging on a cytometer will strengthen any findings or conclusions made as they permit assessment of intracellular staining. Protocols may also need to be adapted depending on the tissue(s) of interest.

Mechanically Induced Bacterial Death Imaged in Real Time: A Simultaneous Nanoindentation and Fluorescence Microscopy Study.

Mechano-bactericidal nanomaterials rely on their mechanical or physical interactions with bacteria and are promising antimicrobial strategies that overcome bacterial resistance. However, the real effect of mechanical versus chemical action on their activity is under debate. In this paper, we quantify the forces necessary to produce critical damage to the bacterial cell wall by performing simultaneous nanoindentation and fluorescence imaging of single bacterial cells. Our experimental setup allows puncturing the cell wall of an immobilized bacterium with the tip of an atomic force microscope (AFM) and following in real time the increase in the fluorescence signal from a cell membrane integrity marker. We correlate the forces exerted by the AFM tip with the fluorescence dynamics for tens of cells, and we find that forces above 20 nN are necessary to exert critical damage. Moreover, a similar experiment is performed in which bacterial viability is assessed through physiological activity, in order to gain a more complete view of the effect of mechanical forces on bacteria. Our results contribute to the quantitative understanding of the interaction between bacteria and nanomaterials.

Investigating lipid mechanisms of MSC immune modulation using metabolic and phenotypic single cell profiling

Background & Aim The immunosuppressive capabilities of human mesenchymal stromal cells (MSCs) have led researchers to explore their potential as therapeutics targeting numerous autoimmune diseases. However, MSC therapies have had limited success so far in clinical trials. Their immune effects are mediated through a complex combination of direct receptor-mediated interactions, vesicle communication and cytokine release mechanisms, making it difficult to identify a unifying underlying biological mechanism of action that could be leveraged to monitor and enhance cell potency. Here, we investigate the role of membrane lipids, a key cell membrane component, associated with these immunosuppressive mechanisms. We aim to evaluate the lipid metabolic profiles of MSCs with known variability in immune regulation and explore the phenotypic changes that occur as a result of differences in lipid signaling. We use longitudinal imaging strategies to directly monitor the associations of cell-cell receptor binding, vesicle release, cytoskeletal network and secretory pathways with immune-related cell activities. Overall, this study aims to directly link lipid metabolism with MSC immunosuppressive behavior using mass spectrometry and image-based approaches, which could be further used to monitor and predict immune response during biomanufacturing of therapeutic cells. Methods, Results & Conclusion MSCs were obtained from cultures with varying immune suppressive activity and secretory profiles. Lipidomic analysis conducted on bulk MSC populations using HPLC/MS/MS revealed several key differences between high and low potency donors. High potency lines showed a negative correlation between sphingomyelin (SM) and ceramide (Cer) whereas the low potency line had a positive correlation indicating that conversion between SM and Cer was associated with cell immune suppression. Multivariate phenotypic imaging analysis of cytoskeletal and vesicle markers showed a strong correlation to cell SM conversion rates. To study heterogeneity of the culture subpopulations, we used Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging to obtain single cell lipid profiles and used advanced deep learning on single cell fluorescent imaging features to understand phenotypic outcomes of lipid signaling. Our findings could have profound implications in understanding immunosuppressive activity of MSCs that could be tuned to enhance the therapeutic efficacy of MSC cultures.

Latent transcriptional variations of individual Plasmodium falciparum uncovered by single-cell RNA-seq and fluorescence imaging.

Malaria parasites follow a complex life cycle that consists of multiple stages that span from the human host to the mosquito vector. Among the species causing malaria, Plasmodium falciparum is the most lethal, with clinical symptoms manifesting during the intraerythrocytic developmental cycle (IDC). During the IDC, P. falciparum progresses through a synchronous and continuous cascade of transcriptional programming previously established using population analyses. While individual parasites are known to exhibit transcriptional variations to evade the host immune system or commit to a sexual fate, such rare expression heterogeneity is largely undetectable on a population level. Therefore, we combined single-cell RNA-sequencing (scRNA-seq) on a microfluidic platform and fluorescence imaging to delineate the transcriptional variations among individual parasites during late asexual and sexual stages. The comparison between asexual and sexual parasites uncovered a set of previously undefined sex-specific genes. Asexual parasites were segregated into three distinct clusters based on the differential expression of genes encoding SERAs, rhoptry proteins, and EXP2 plus transporters. Multiple pseudotime analyses revealed that these stage-specific transitions are distinct. RNA fluorescent in situ hybridization of cluster-specific genes validated distinct stage-specific expression and transitions during the IDC and defined the highly variable transcriptional pattern of EXP2. Additionally, these analyses indicated huge variations in the stage-specific transcript levels among parasites. Overall, scRNA-seq and RNA-FISH of P. falciparum revealed distinct stage transitions and unexpected degrees of heterogeneity with potential impact on transcriptional regulation during the IDC and adaptive responses to the host.