Comparison of No Tap (two-step) and tapping robotic assisted cortical bone trajectory screw insertion.

Workflow for cortical bone trajectory (CBT) screws includes tapping line-to-line or under tapping by 1 mm. We describe a non-tapping, two-step workflow for CBT screw placement, and compare the safety profile and time savings to the Tap (three-step) workflow. Patients undergoing robotic assisted 1-3 level posterior fusion with CBT screws for degenerative conditions were identified and separated into either a No-Tap or Tap workflow. Number of total screws, screw-related complications, estimated blood loss, operative time, robotic time, and return to the operating room were collected and analyzed. There were 91 cases (458 screws) in the No-Tap and 88 cases (466 screws) in the Tap groups, with no difference in demographics, revision status, ASA grade, approach, number of levels fused or diagnosis between cohorts. Total robotic time was lower in the No-Tap (26.7 min) versus the Tap group (30.3 min, p = 0.053). There was no difference in the number of malpositioned screws identified intraoperatively (10 vs 6, p = 0.427), screws converted to freehand (3 vs 3, p = 0.699), or screws abandoned (3 vs 2, p = 1.000). No pedicle/pars fracture or fixation failure was seen in the No-Tap cohort and one in the Tap cohort (p = 1.00). No patients in either cohort were returned to OR for malpositioned screws. This study showed that the No-Tap screw insertion workflow for robot-assisted CBT reduces robotic time without increasing complications.

Artificial intelligence-powered optimization of KI-67 assessment in breast cancer: enhancing precision and workflow efficiency. a literature review.

Breast Cancer (BC) has evolved from traditional morphological analysis to molecular profiling, identifying new subtypes. Ki-67, a prognostic biomarker, helps classify subtypes and guide chemotherapy decisions. This review explores how artificial intelligence (AI) can optimize Ki-67 assessment, improving precision and workflow efficiency in BC management. The study presents a critical analysis of the current state of AI-powered Ki-67 assessment. Results demonstrate high agreement between AI and standard Ki-67 assessment methods highlighting AI's potential as an auxiliary tool for pathologists. Despite these advancements, the review acknowledges limitations such as the restricted timeframe and diverse study designs, emphasizing the need for further research to address these concerns. In conclusion, AI holds promise in enhancing Ki-67 assessment's precision and workflow efficiency in BC diagnosis. While challenges persist, the integration of AI can revolutionize BC care, making it more accessible and precise, even in resource-limited settings.

Some tips and tricks for a Correlative Light Electron Microscopy workflow using stable expression of fluorescent proteins.

Correlative Light Electron Microscopy (CLEM) encompasses a wide range of experimental approaches with different degrees of complexity and technical challenges where the attributes of both light and electron microscopy are combined in a single experiment. Although the biological question always determines what technology is the most appropriate, we generally set out to apply the simplest workflow possible. For 2D cell cultures expressing fluorescently tagged molecules, we report on a simple and very powerful CLEM approach by using gridded finder imaging dishes. We first determine the gross localization of the fluorescence using light microscopy and subsequently we retrace the origin/localization of the fluorescence by projecting it onto the ultrastructural reference space obtained by transmission electron microscopy (TEM). Here we describe this workflow and highlight some basic principles of the sample preparation for such a simple CLEM experiment. We will specifically focus on the steps following the resin embedding for TEM and the introduction of the sample in the electron microscope.

How to edit a surgical case video.

A video can help highlight the real-time steps, anatomy and the technical aspects of a case that may be difficult to convey with text or static images alone. Editing with a regimented workflow allows for the transmission of only essential information to the viewer while maximizing efficiency by going through the editing process. This video tutorial breaks down the fundamentals of surgical video editing with tips and pointers to simplify the workflow.

MetaboAnalystR 4.0: a unified LC-MS workflow for global metabolomics.

The wide applications of liquid chromatography - mass spectrometry (LC-MS) in untargeted metabolomics demand an easy-to-use, comprehensive computational workflow to support efficient and reproducible data analysis. However, current tools were primarily developed to perform specific tasks in LC-MS based metabolomics data analysis. Here we introduce MetaboAnalystR 4.0 as a streamlined pipeline covering raw spectra processing, compound identification, statistical analysis, and functional interpretation. The key features of MetaboAnalystR 4.0 includes an auto-optimized feature detection and quantification algorithm for LC-MS1 spectra processing, efficient MS2 spectra deconvolution and compound identification for data-dependent or data-independent acquisition, and more accurate functional interpretation through integrated spectral annotation. Comprehensive validation studies using LC-MS1 and MS2 spectra obtained from standards mixtures, dilution series and clinical metabolomics samples have shown its excellent performance across a wide range of common tasks such as peak picking, spectral deconvolution, and compound identification with good computing efficiency. Together with its existing statistical analysis utilities, MetaboAnalystR 4.0 represents a significant step toward a unified, end-to-end workflow for LC-MS based global metabolomics in the open-source R environment.

Improving routine use of clinical pathway decision support through integration of an EHR with a clinical library resource designed to provide evidence-based guidance within oncology workflows.

BACKGROUND: The rapid evolution, complexity, and specialization of oncology treatment makes it challenging for physicians to provide care based on the latest and best evidence. We hypothesized that physicians would use evidence-based trusted care pathways if they were easy to use and integrated into clinical workflow at the point of care. METHODS: Within a large integrated care delivery system, we assembled clinical experts to define and update drug treatment pathways, encoded them as flowcharts in an online library integrated with the electronic medical record, communicated expectations that clinicians would use these pathways for every eligible patient, and combined data from multiple sources to understand usage over time. RESULTS: We were able to achieve > 75% utilization of eligible protocols ordered through these pathways within two years, with > 90% of individual oncologists having consulted the pathway at least once, despite no requirements or external incentives associated with pathway usage. Feedback from users contributed to improvements and updates to the guidance. CONCLUSIONS: By making our clinical decision support easily accessible and actionable, we find that we have made considerable progress toward our goal of having physicians consult the latest evidence in their treatment decisions.

SNP-SVant: A Computational Workflow to Predict and Annotate Genomic Variants in Organisms Lacking Benchmarked Variants.

Whole-genome sequencing is widely used to investigate population genomic variation in organisms of interest. Assorted tools have been independently developed to call variants from short-read sequencing data aligned to a reference genome, including single nucleotide polymorphisms (SNPs) and structural variations (SVs). We developed SNP-SVant, an integrated, flexible, and computationally efficient bioinformatic workflow that predicts high-confidence SNPs and SVs in organisms without benchmarked variants, which are traditionally used for distinguishing sequencing errors from real variants. In the absence of these benchmarked datasets, we leverage multiple rounds of statistical recalibration to increase the precision of variant prediction. The SNP-SVant workflow is flexible, with user options to tradeoff accuracy for sensitivity. The workflow predicts SNPs and small insertions and deletions using the Genome Analysis ToolKit (GATK) and predicts SVs using the Genome Rearrangement IDentification Software Suite (GRIDSS), and it culminates in variant annotation using custom scripts. A key utility of SNP-SVant is its scalability. Variant calling is a computationally expensive procedure, and thus, SNP-SVant uses a workflow management system with intermediary checkpoint steps to ensure efficient use of resources by minimizing redundant computations and omitting steps where dependent files are available. SNP-SVant also provides metrics to assess the quality of called variants and converts between VCF and aligned FASTA format outputs to ensure compatibility with downstream tools to calculate selection statistics, which are commonplace in population genomics studies. By accounting for both small and large structural variants, users of this workflow can obtain a wide-ranging view of genomic alterations in an organism of interest. Overall, this workflow advances our capabilities in assessing the functional consequences of different types of genomic alterations, ultimately improving our ability to associate genotypes with phenotypes. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Predicting single nucleotide polymorphisms and structural variations Support Protocol 1: Downloading publicly available sequencing data Support Protocol 2: Visualizing variant loci using Integrated Genome Viewer Support Protocol 3: Converting between VCF and aligned FASTA formats.

Workflow for detecting biomedical articles with underlying open and restricted-access datasets.

To monitor the sharing of research data through repositories is increasingly of interest to institutions and funders, as well as from a meta-research perspective. Automated screening tools exist, but they are based on either narrow or vague definitions of open data. Where manual validation has been performed, it was based on a small article sample. At our biomedical research institution, we developed detailed criteria for such a screening, as well as a workflow which combines an automated and a manual step, and considers both fully open and restricted-access data. We use the results for an internal incentivization scheme, as well as for a monitoring in a dashboard. Here, we describe in detail our screening procedure and its validation, based on automated screening of 11035 biomedical research articles, of which 1381 articles with potential data sharing were subsequently screened manually. The screening results were highly reliable, as witnessed by inter-rater reliability values of ≥0.8 (Krippendorff's alpha) in two different validation samples. We also report the results of the screening, both for our institution and an independent sample from a meta-research study. In the largest of the three samples, the 2021 institutional sample, underlying data had been openly shared for 7.8% of research articles. For an additional 1.0% of articles, restricted-access data had been shared, resulting in 8.3% of articles overall having open and/or restricted-access data. The extraction workflow is then discussed with regard to its applicability in different contexts, limitations, possible variations, and future developments. In summary, we present a comprehensive, validated, semi-automated workflow for the detection of shared research data underlying biomedical article publications.

An untargeted analytical workflow based on Kendrick mass defect filtering reveals dysregulations in acylcarnitines in prostate cancer tissue.

BACKGROUND: Metabolomics is nowadays considered one the most powerful analytical for the discovery of metabolic dysregulations associated with the insurgence of cancer, given the reprogramming of the cell metabolism to meet the bioenergetic and biosynthetic demands of the malignant cell. Notwithstanding, several challenges still exist regarding quality control, method standardization, data processing, and compound identification. Therefore, there is a need for effective and straightforward approaches for the untargeted analysis of structurally related classes of compounds, such as acylcarnitines, that have been widely investigated in prostate cancer research for their role in energy metabolism and transport and ß-oxidation of fatty acids. RESULTS: In the present study, an innovative analytical platform was developed for the straightforward albeit comprehensive characterization of acylcarnitines based on high-resolution mass spectrometry, Kendrick mass defect filtering, and confirmation by prediction of their retention time in reversed-phase chromatography. In particular, a customized data processing workflow was set up on Compound Discoverer software to enable the Kendrick mass defect filtering, which allowed filtering out more than 90 % of the initial features resulting from the processing of 25 tumoral and adjacent non-malignant prostate tissues collected from patients undergoing radical prostatectomy. Later, a partial least square-discriminant analysis model validated by repeated double cross-validation was built on the dataset of 74 annotated acylcarnitines, with classification rates higher than 93 % for both groups, and univariate statistical analysis helped elucidate the individual role of the annotated metabolites. SIGNIFICANCE: Hydroxylation of short- and medium-chain minor acylcarnitines appeared to be a significant variable in describing tissue differences, suggesting the hypothesis that the neoplastic growth is linked to oxidation phenomena on selected metabolites and reinforcing the need for effective methods for the annotation of minor metabolites.

Optimizing differential expression analysis for proteomics data via high-performing rules and ensemble inference.

Identification of differentially expressed proteins in a proteomics workflow typically encompasses five key steps: raw data quantification, expression matrix construction, matrix normalization, missing value imputation (MVI), and differential expression analysis. The plethora of options in each step makes it challenging to identify optimal workflows that maximize the identification of differentially expressed proteins. To identify optimal workflows and their common properties, we conduct an extensive study involving 34,576 combinatoric experiments on 24 gold standard spike-in datasets. Applying frequent pattern mining techniques to top-ranked workflows, we uncover high-performing rules that demonstrate optimality has conserved properties. Via machine learning, we confirm optimal workflows are indeed predictable, with average cross-validation F1 scores and Matthew's correlation coefficients surpassing 0.84. We introduce an ensemble inference to integrate results from individual top-performing workflows for expanding differential proteome coverage and resolve inconsistencies. Ensemble inference provides gains in pAUC (up to 4.61%) and G-mean (up to 11.14%) and facilitates effective aggregation of information across varied quantification approaches such as topN, directLFQ, MaxLFQ intensities, and spectral counts. However, further development and evaluation are needed to establish acceptable frameworks for conducting ensemble inference on multiple proteomics workflows.

OMD Curation Toolkit: a workflow for in-house curation of public omics datasets.

BACKGROUND: Major advances in sequencing technologies and the sharing of data and metadata in science have resulted in a wealth of publicly available datasets. However, working with and especially curating public omics datasets remains challenging despite these efforts. While a growing number of initiatives aim to re-use previous results, these present limitations that often lead to the need for further in-house curation and processing. RESULTS: Here, we present the Omics Dataset Curation Toolkit (OMD Curation Toolkit), a python3 package designed to accompany and guide the researcher during the curation process of metadata and fastq files of public omics datasets. This workflow provides a standardized framework with multiple capabilities (collection, control check, treatment and integration) to facilitate the arduous task of curating public sequencing data projects. While centered on the European Nucleotide Archive (ENA), the majority of the provided tools are generic and can be used to curate datasets from different sources. CONCLUSIONS: Thus, it offers valuable tools for the in-house curation previously needed to re-use public omics data. Due to its workflow structure and capabilities, it can be easily used and benefit investigators in developing novel omics meta-analyses based on sequencing data.

Slimmable transformer with hybrid axial-attention for medical image segmentation.

The transformer architecture has achieved remarkable success in medical image analysis owing to its powerful capability for capturing long-range dependencies. However, due to the lack of intrinsic inductive bias in modeling visual structural information, the transformer generally requires a large-scale pre-training schedule, limiting the clinical applications over expensive small-scale medical data. To this end, we propose a slimmable transformer to explore intrinsic inductive bias via position information for medical image segmentation. Specifically, we empirically investigate how different position encoding strategies affect the prediction quality of the region of interest (ROI) and observe that ROIs are sensitive to different position encoding strategies. Motivated by this, we present a novel Hybrid Axial-Attention (HAA) that can be equipped with pixel-level spatial structure and relative position information as inductive bias. Moreover, we introduce a gating mechanism to achieve efficient feature selection and further improve the representation quality over small-scale datasets. Experiments on LGG and COVID-19 datasets prove the superiority of our method over the baseline and previous works. Internal workflow visualization with interpretability is conducted to validate our success better; the proposed slimmable transformer has the potential to be further developed into a visual software tool for improving computer-aided lesion diagnosis and treatment planning.

Streamlining neuroradiology workflow with AI for improved cerebrovascular structure monitoring.

Radiological imaging to examine intracranial blood vessels is critical for preoperative planning and postoperative follow-up. Automated segmentation of cerebrovascular anatomy from Time-Of-Flight Magnetic Resonance Angiography (TOF-MRA) can provide radiologists with a more detailed and precise view of these vessels. This paper introduces a domain generalized artificial intelligence (AI) solution for volumetric monitoring of cerebrovascular structures from multi-center MRAs. Our approach utilizes a multi-task deep convolutional neural network (CNN) with a topology-aware loss function to learn voxel-wise segmentation of the cerebrovascular tree. We use Decorrelation Loss to achieve domain regularization for the encoder network and auxiliary tasks to provide additional regularization and enable the encoder to learn higher-level intermediate representations for improved performance. We compare our method to six state-of-the-art 3D vessel segmentation methods using retrospective TOF-MRA datasets from multiple private and public data sources scanned at six hospitals, with and without vascular pathologies. The proposed model achieved the best scores in all the qualitative performance measures. Furthermore, we have developed an AI-assisted Graphical User Interface (GUI) based on our research to assist radiologists in their daily work and establish a more efficient work process that saves time.

3D printing vs traditional workflow for the fabrication of mandibular implant overdentures: study protocol for a mixed-methods cross-over RCT.

BACKGROUND: Complete tooth loss is a significant global oral health issue, particularly impacting older individuals with lower socioeconomic status. Computer-assisted technologies enhance oral healthcare access by the elderly. Despite promising in vitro reports on digital denture materials, evidence from randomized clinical trials (RCTs) is lacking to verify their performance. This cross-over RCT will investigate whether 3D-printed implant-retained mandibular overdentures (IMO) are more satisfactory for edentulous seniors than those made through traditional methods. METHODS/DESIGN: We will recruit 26 completely edentulous participants (any sex/gender) based on the following eligibility criteria: age ≥ 60 years, no tooth extraction in the past 12 months, two implants in the lower jaw, and need for new dentures in both jaws. Each participant will receive two denture pairs, either manufactured by 3D printing or traditionally, to be worn in a random order. A timeline of 3 months with each denture pair will be considered for outcome assessment (total: 6 months). Patient satisfaction with dentures will be measured by the McGill Denture Satisfaction Questionnaire. We will evaluate other patient-reported outcomes (including oral health-related quality of life) as well as clinician-assessed quality and cost. At the end of the trial, participants will choose which denture pair they wish to keep and interviewed about their experiences with the 3D-printed IMO. The quantitative and qualitative data will be incorporated through an explanatory mixed-methods strategy. A final quantitative assessment will happen after 12 months with the preferred IMO to assess the long-term performance and maintenance needs. DISCUSSION: This mixed-methods RCT will explore patient experiences with 3D-printed IMOs, aiming to assess the potential for altering clinical practice and dental public health policies. Our results will inform policies by showing whether 3D printing offers comparable outcomes at lower costs, facilitating greater access to oral care for the elderly. TRIAL REGISTRATION: ClinicalTrials.gov, NCT06155630, Registered on 04 December 2023. https://classic. CLINICALTRIALS: gov/ct2/show/NCT06155630.

Sample Preparation and Phosphopeptide Enrichment for Plant Phosphoproteomics via Label-Free Mass Spectrometry.

Phosphopeptide enrichment is the main bottleneck of every phosphorylation study. Therefore, in this chapter, a general workflow tries to overbridge the hurdles of plant sample handling from sample collection to protein extraction, protein solubilization, enzymatic digestion, and enrichment step prior to mass spectrometry. The workflow provides information to perform global proteomics as well as phosphoproteomics enabling the researcher to use the protocol in both fields.

In-Depth Retinal Sensitivity Assessment With the MP3 Type S Microperimeter: A Methods Study.

Purpose: Retinal sensitivity is frequently listed as an end point in clinical trials, often with long working practices. The purpose of this methods study was to provide a new workflow and reduced test time for in-depth characterization of retinal sensitivity. Methods: A workflow for the MP3-S microperimeter with detailed functional characterization of the retina under photopic, mesopic, and scotopic conditions was evaluated. Grids of 32 and 28 test positions for photopic/mesopic and scotopic, respectively, were tested in 12 healthy individuals and compared with an established 68-point grid for test time, mean sensitivity (MS), and bivariate contour ellipse area (BCEA). Results: The mean test time (range; ±SD) was 10.5 minutes (8.4-14.9; ±2.0) in the 68-point grid and 4.3 minutes (3.8-5.0; ±0.4) in the 32-point grid, which was significantly different (P < 0.0001). The mean of difference in test time (±SD; 95% confidence interval) was 6.1 minutes (±2.0; 4.6-7.6). MS and BCEA were significantly correlated between grids (r = 0.89 and 0.74; P = 0.0005 and 0.014, respectively). Mean test time of subjects who underwent the full protocol (n = 4) was 2.15 hours. Conclusions: The protocol suggested herein appears highly feasible with in-depth characterization of retinal function under different testing conditions and in a short test time. Translational Relevance: The protocol described herein allows for characterization of the retina under different testing conditions and in a short test time, which is relevant due to its potential for patient prognostication and follow-up in clinical settings and also given its increasing role as a clinical trial end point.

Standardised Versioning of Datasets: a FAIR-compliant Proposal.

This paper presents a standardised dataset versioning framework for improved reusability, recognition and data version tracking, facilitating comparisons and informed decision-making for data usability and workflow integration. The framework adopts a software engineering-like data versioning nomenclature ("major.minor.patch") and incorporates data schema principles to promote reproducibility and collaboration. To quantify changes in statistical properties over time, the concept of data drift metrics (d) is introduced. Three metrics (dP, dE,PCA, and dE,AE) based on unsupervised Machine Learning techniques (Principal Component Analysis and Autoencoders) are evaluated for dataset creation, update, and deletion. The optimal choice is the dE,PCA metric, combining PCA models with splines. It exhibits efficient computational time, with values below 50 for new dataset batches and values consistent with seasonal or trend variations. Major updates (i.e., values of 100) occur when scaling transformations are applied to over 30% of variables while efficiently handling information loss, yielding values close to 0. This metric achieved a favourable trade-off between interpretability, robustness against information loss, and computation time.

Effect of different fabrication workflows on the passive fit of screw-retained bar splinting two interforaminal implants: a parallel blinded randomised clinical trial.

BACKGROUND: To clinically compare the effect of the conventional and the digital workflows on the passive fit of a screw retained bar splinting two inter-foraminal implants. METHODS: The current study was designed to be a parallel triple blinded randomised clinical trial. Thirty six completely edentulous patients were selected and simply randomized into two groups; conventional group (CG) and digital group (DG). The participants, investigator and outcome assessor were blinded. In the group (CG), the bar was constructed following a conventional workflow in which an open top splinted impression and a lost wax casting technology were used. However, in group (DG), a digital workflow including a digital impression and a digital bar milling technology was adopted. Passive fit of each bar was then evaluated clinically by applying the screw resistance test using the "flag" technique in the passive and non passive situations. The screw resistance test parameter was also calculated. Unpaired t-test was used for intergroup comparison. P-value < 0.05 was the statistical significance level. The study protocol was reviewed by the Research Ethics Committee in the author's university (Rec IM051811). Registration of the clinical trial was made on clinical trials.gov ID NCT05770011. An informed consent was obtained from all participants. RESULTS: Non statistically significant difference was denoted between both groups in all situations. In the passive situation, the mean ± standard deviation values were 1789.8° ± 20.7 and1786.1° ± 30.7 for the groups (CG) and (DG) respectively. In the non passive situation, they were 1572.8° ± 54.2 and 1609.2° ± 96.9. Regarding the screw resistance test parameter, they were 217° ± 55.3 and 176° ± 98.8. CONCLUSION: Conventional and digital fabrication workflows had clinically comparable effect on the passive fit of screw retained bar attachments supported by two dental implants.

Deep learning workflow to support in-flight processing of digital aerial imagery for wildlife population surveys.

Deep learning shows promise for automating detection and classification of wildlife from digital aerial imagery to support cost-efficient remote sensing solutions for wildlife population monitoring. To support in-flight orthorectification and machine learning processing to detect and classify wildlife from imagery in near real-time, we evaluated deep learning methods that address hardware limitations and the need for processing efficiencies to support the envisioned in-flight workflow. We developed an annotated dataset for a suite of marine birds from high-resolution digital aerial imagery collected over open water environments to train the models. The proposed 3-stage workflow for automated, in-flight data processing includes: 1) image filtering based on the probability of any bird occurrence, 2) bird instance detection, and 3) bird instance classification. For image filtering, we compared the performance of a binary classifier with Mask Region-based Convolutional Neural Network (Mask R-CNN) as a means of sub-setting large volumes of imagery based on the probability of at least one bird occurrence in an image. On both the validation and test datasets, the binary classifier achieved higher performance than Mask R-CNN for predicting bird occurrence at the image-level. We recommend the binary classifier over Mask R-CNN for workflow first-stage filtering. For bird instance detection, we leveraged Mask R-CNN as our detection framework and proposed an iterative refinement method to bootstrap our predicted detections from loose ground-truth annotations. We also discuss future work to address the taxonomic classification phase of the envisioned workflow.

CITEViz: interactively classify cell populations in CITE-Seq via a flow cytometry-like gating workflow using R-Shiny.

BACKGROUND: The rapid advancement of new genomic sequencing technology has enabled the development of multi-omic single-cell sequencing assays. These assays profile multiple modalities in the same cell and can often yield new insights not revealed with a single modality. For example, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) simultaneously profiles the RNA transcriptome and the surface protein expression. The surface protein markers in CITE-Seq can be used to identify cell populations similar to the iterative filtration process in flow cytometry, also called "gating", and is an essential step for downstream analyses and data interpretation. While several packages allow users to interactively gate cells, they often do not process multi-omic sequencing datasets and may require writing redundant code to specify gate boundaries. To streamline the gating process, we developed CITEViz which allows users to interactively gate cells in Seurat-processed CITE-Seq data. CITEViz can also visualize basic quality control (QC) metrics allowing for a rapid and holistic evaluation of CITE-Seq data. RESULTS: We applied CITEViz to a peripheral blood mononuclear cell CITE-Seq dataset and gated for several major blood cell populations (CD14 monocytes, CD4 T cells, CD8 T cells, NK cells, B cells, and platelets) using canonical surface protein markers. The visualization features of CITEViz were used to investigate cellular heterogeneity in CD14 and CD16-expressing monocytes and to detect differential numbers of detected antibodies per patient donor. These results highlight the utility of CITEViz to enable the robust classification of single cell populations. CONCLUSIONS: CITEViz is an R-Shiny app that standardizes the gating workflow in CITE-Seq data for efficient classification of cell populations. Its secondary function is to generate basic feature plots and QC figures specific to multi-omic data. The user interface and internal workflow of CITEViz uniquely work together to produce an organized workflow and sensible data structures for easy data retrieval. This package leverages the strengths of biologists and computational scientists to assess and analyze multi-omic single-cell datasets. In conclusion, CITEViz streamlines the flow cytometry gating workflow in CITE-Seq data to help facilitate novel hypothesis generation.