Search Results for: automated slide scanner

Citation: Mehralivand S, et al. Academic Radiology 2022 Code Availability: https://github.com/Project-MONAI/research-contributions/tree/main/prostate-mri-lesion-seg

Employing spatial biology techniques enables acquisition of transcript and protein data from intact tissue sections, and in turn, spatial distribution information and cellular interaction patterns are revealed.

There are many tools and strategies available for cell annotation. I've included a non-comprehensive list for your convenience: Azimuth SingleR scType Garnet Digital Cell Sorter . Cell Marker 2.0 Here is a list of resources that Read More...

The LCBG Microscopy Core offers imaging technologies and training. The Core has established instrumentation for for 2D and 3D imaging of both fixed and living specimens.

Profile the entire transcriptome and more than 570 proteins on a single slide with the GeoMx Digital Spatial Profiler

Techniques The Laboratory of Cancer Biology and Genetics Microscopy Core houses multiple systems that can be used to analyze cell structure, protein expression, and cell dynamics using immunofluorescence. These include inverted epifluorescence microscopes, a confocal Read More...

New versions of Bioconductor are released every 6 months and work with a specific version of R. Because of this release schedule and associated automated testing, "each Bioconductor release provides a suite of packages that Read More...

06/01/2023 - CellTypist was first developed as a platform for exploring tissue adaptation of cell types using scRNA-seq semi-automatic annotations. Now it's an open source tool for automated cell type annotations as well as a  Read More...

New versions of Bioconductor are released every 6 months and work with a specific version of R. Because of this release schedule and associated automated testing, "each Bioconductor release provides a suite of packages that Read More...

09/23/2021 - Meeting Link: https://cbiit.webex.com/cbiit/j.php?MTID=m5fa0e43ae167ed5ea3a77fb25d339a82 TOPIC: AI for Multimodal Data, presented by members of the Strategic Data Science Initiative, Read More...

Let's plot the same data using geom_boxplot().A boxplot can be used to summarize the distribution of a numeric variable across groups. ::: {.cell output-location='slide'} ggplot(data=exdata) + geom_boxplot(aes(x=Treatment, Read More...

This exercise will use Seaborn's clustermap function to construct a gene expression heatmap of top differentially expressed genes in the HBR and UHR study. Heatmaps are another common visualization in RNA sequencing and allow Read More...

This exercise will use Seaborn's clustermap function to construct a gene expression heatmap of top differentially expressed genes in the HBR and UHR study. Heatmaps are another common visualization in RNA sequencing and allow Read More...

Imported using Python Contains RNA sequencing gene expression counts where the columns are: First column (not labeled) contains gene names Columns 2 through 7 contains expression counts for each genes across the six samples See next slide

Imported using Python Contains RNA sequencing gene expression counts where the columns are: First column (not labeled) contains gene names Columns 2 through 7 contains expression counts for each genes across the six samples See next slide

We can see how easy it is to change the way the data is plotted. Let's plot the same data using geom_line(). ::: {.cell output-location='slide'} ggplot(data=exdata) + geom_line(aes(x=Number. Read More...

If the slideshow is opened in print mode, the chalkboard drawings in the session storage (see storage option - print version must be opened in the same tab or window as the original slideshow) or Read More...

The Mouse Imaging Facility (MIF) is a shared, trans-NIH intramural resource for animal imaging studies. MIF provides access to state-of-the-art radiological imaging methods optimized for mice, rats, other animals, and tissue samples. MIF provides intellectual, Read More...

What is Visium FFPE v2 with CytAssist? Visium FFPE v2 is sequencing-based spatial profiling technology developed by 10x Genomics. This assay can take mouse or human tissue sections on normal glass slides as input and Read More...

Bruker AVANCE 400 and 500 MHz NMR instruments. Helium Cryoprobe technology on the 500 MHz machine for added sensitivity, especially for Carbon-13 spectra. Access to a second 500 MHz instrument with Prodigy Liquid Nitrogen-cooled cryoprobe. User Accounts can be Read More...

04/10/2025 - This one hour online training introduces participants to the tools and techniques for analyzing and quantifying microscopy images using MATLAB’s low-code algorithms. Participants will learn how to preprocess images, segment regions Read More...

07/25/2024 - Join us for an informative webinar on the GARDE software where Dr. Del Fiol will describe how GARDE works, how GARDE has been implemented to support population-based genetic testing, the GARDE chatbot, and results Read More...

To load a single file, we use W10

05/14/2024 - Participants will learn how to develop artificial intelligence (AI) applications using MATLAB, even if they do not have a formal background in machine and deep learning. The goal of this course is to introduce Read More...

09/28/2023 - Attend the Bridge2AI-Skills & Workforce Development (SWD) Lecture Series for 2023-24 on the Large Language Model (LLM) Module Dr. Xia “Ben” Hu is an Associate Professor at Rice University in the Department of Read More...

High resolution single cell profiling assays have provided an unprecedented view of many biological systems and processes, but the spatial context in which this biology is occurring is often crucial. Spatial profiling, including spatial transcriptomic Read More...

05/15/2023 - Participants will learn how to develop artificial intelligence (AI) applications using MATLAB, even if they do not have a formal background in machine and deep learning. The goal of this course is to introduce Read More...

11/18/2021 - In this class, we will explore the basics of R. Topics covered will include: Overview of R Studio IDE Checking R version and switching between different versions of R Working with directories Setting working Read More...

11/12/2021 - The Cancer Genomics Cloud (CGC) is a cloud-based bioinformatics ecosystem supported by the National Cancer Institute (NCI). The CGC allows users to run computational workflows defined in the Common Workflow Language (CWL) on a Read More...

09/24/2021 - Participants will learn how to develop artificial intelligence (AI) applications using MATLAB, even if they do not have a formal background in machine and deep learning. The goal of this course is to introduce Read More...

09/23/2021 - Registration: https://btep.ccr.cancer.gov/classes/ai_four/ Meeting Link: https://cbiit.webex.com/cbiit/j.php?MTID=m5fa0e43ae167ed5ea3a77fb25d339a82 Description: In this talk, we Read More...

10/20/2020 - Participants will learn how to develop artificial intelligence (AI) applications using MATLAB, even if they do not have a formal background in machine and deep learning. The goal of this course is to introduce Read More...

02/27/2020 - In this symposium, distinguished scientists will share recent successes in their research to visualize RNA targets at the single molecule level with single cell resolution and morphological context. Here are some of the exciting Read More...

There are many defaults when generating a plot with ggplot2, but almost everything you see can be customized. :::: {.columns} ::: {.column width="30%"} Here we can see: Assigned colors A legend axis titles a plot Read More...

The first example will use Python code to demonstrate the utility of Jupyter Notebook for keeping code, output, and analysis steps all in one place. First, the import command of Python will be used to Read More...

The first example will use Python code to demonstrate the utility of Jupyter Notebook for keeping code, output, and analysis steps all in one place. First, the import command of Python will be used to Read More...

Imported using R and Python Contains RNA sequencing differential expression analysis results. The columns are: name: contains gene names log2FoldChange: gene expression change between two experimental conditions on the log2 scale PAdj: adjusted p-value Read More...

Imported using R and Python Contains RNA sequencing differential expression analysis results. The columns are: name: contains gene names log2FoldChange: gene expression change between two experimental conditions on the log2 scale PAdj: adjusted p-value Read More...

::: {.cell output-location='slide'} ggplot(exdata) + geom_point(aes(x=Number.of.Transcripts, y = Total.Counts, fill=Treatment), shape=21,size=3) + #can change labels of fill levels along with colors scale_fill_manual(values=c("purple& Read More...

There are a number of ways to specify the color argument including by name, number, and hex code. Here is a great resource from the R Graph Gallery for assigning colors in R. There are Read More...

Is there a relationship between treatment ("dex") and the number of transcripts or total counts? ::: {.cell output-location='slide'} #adding the color argument to our mapping aesthetic ggplot(exdata) + geom_point(aes(x=Number. Read More...

Colors are assigned to the fill and color aesthetics in aes(). We can change the default colors by providing an additional layer to our figure. To change the color, we use the scale_color functions: Read More...

What is the relationship between total transcript sums per sample and the number of recovered transcripts per sample? ::: {.cell output-location='slide'} #let's plot our data ggplot(data=exdata) + geom_point(aes(x=Number.of. Read More...

Aesthetics that are not mapped to our variables are placed outside of the aes() function. These aesthetics are manually assigned and do not undergo the same scaling process as those within aes(). ::: {.cell output-location='slide'} # Read More...

Biostars: Bioinformatics Explained is a question and answer forum where researchers can obtain answers to questions ranging from simple to advanced in the fields of bioinformatics, computational genomics, and biological data analysis. The developers of Read More...

The plugin has several configuration options: boardmarkerWidth: an integer, the drawing width of the boardmarker; larger values draw thicker lines. chalkWidth: an integer, the drawing width of the chalk; larger values draw thicker lines. chalkEffect: Read More...

Software that offers simple yet powerful tools for copy number (CNV) and sequence variation analysis and visualization from aCGH, SNP arrays as well as NGS WES/WGS and expression data. Nexus Copy Number – Accelerating Copy Read More...

Our operational objectives are to provide state-of-the-art OMICS technologies in support of the Genetics Branch (GB) investigators and collaborators. Research Services Wet Lab Single cell isolation from fresh, frozen, and FFPE tissue, DNA/RNA extractions Read More...

The NCI High-Throughput Imaging Facility (HiTIF) works in a collaborative fashion with NCI/NIH Investigators by providing them with the necessary expertise, instrumentation, and software to develop and execute advanced High-Throughput Imaging (HTI) assays. These Read More...

The NMR Facility for Biological Research operates six NMR spectrometers with proton resonance frequencies from 850 to 500 MHz. Three of the highest field spectrometers (850, 700, 600) are equipped with higher sensitivity cryoprobes optimized for high-resolution multi-dimensional and relaxation Read More...

The primary objective of the Protein Technology Core (PTC) is to establish an experimental screening pipeline for single-domain antibodies termed nanobodies. Nanobodies are antibody fragments consisting of a single monomeric variable antibody domain. The PTC, Read More...

Biomarker Discovery with Morphological Context:  Changing how tissue specimens are analyzed < https://youtu.be/mVhfZq8ppbc What is Digital Spatial Profiling? GeoMx Digital Spatial Profiler is a novel platform developed by NanoString. Digital Spatial Read More...

NanoString Technology The nCounter® Analysis System is an automated, multi-application, digital detection and counting system which directly profiles up to 800 molecules simultaneously from a single sample using a novel barcoding technology. Profile hundreds of mRNAs, Read More...

The FNLCR Molecular Histopathology Laboratory (MHL) provides comprehensive veterinary pathology support for animal health monitoring, biomarker discovery and validation, drug development, genomics, and proteomics on a cost recovered basis. The MHL is organized into multiple Read More...

The Crystallization Facility provides an automated environment for setting up crystallization experiments in a high-throughput format, storing the resulting plates under controlled conditions, and monitoring the status of prepared droplets remotely. The Facility is in Read More...

OSTR provides CCR investigators with access to a variety of software licenses for genomic, proteomic, pathway analysis and data visualization tools. These software are funded by OSTR and made available at no cost to CCR Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Extramural Common Fund Resources Metabolomics Workbench Developed by the NIH Metabolomics Common Fund's National Metabolomics Data Repository ( Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Intramural CryoEM (NICE) Consortium NICE provides NCI, NIAID, NIEHS, NICHD, NIDCR, NEI, and NIA investigators with Read More...

The Center for Inherited Disease Research (CIDR)'s  mission is to support the genetics community by providing high-quality, cutting-edge genomics services and technologies in order to expand our understanding of disease and catalyze discoveries that Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New Resources on CREx Interested in imaging large scale biological samples?  Volume electron microscopy allows for Read More...

07/15/2025 - Single-cell technologies enable the discovery of many novel cell phenotypes, but this growing body of knowledge remains fragmented across the scientific literature. Natural language processing (NLP) offers a promising approach to extract this information Read More...

This is part II of the article highlighting nf-core pipelines and specifically addresses the use of these pipelines in the DNAnexus cloud environment. Part I of the article can be found in the October 2023 topic Read More...

07/11/2024 - Please join us for this special event featuring three speakers on the topic of Single-Cell Spatial Transcriptomics. George Zaki, Ph.D., Director, Applied Scientific Computing, BACS, The Frederick National Lab for Cancer Research, NCI/ Read More...

The Advanced Biomedical Computational Science (ABCS) group focuses on applications of bioinformatics, computational and data science, and artificial intelligence to support NCI researchers. ABCS provides: • Subject matter expertise in genomics, proteomics, and imaging. • Machine learning/ Read More...

03/22/2024 - This 3-hour seminar is tailored for biologists, data analysts, and researchers who are eager to dive into the essentials of computational flow cytometry analysis using R. Flow cytometry is a crucial technique in cell Read More...

The identification of cell types in single cell genomics data (cell type&nbsp;annotation) can provide new insights into cellular identities, heterogeneity, and functional roles. Cell type&nbsp;annotation&nbsp;is challenging Read More...

05/17/2022 - Metabolomic and multi-omic data are increasingly being collected in basic, preclinical, and clinical research studies. Interpretation of these data though remains challenging.  Common challenges include the difficulty in identifying metabolites and assigning unique identifiers, Read More...

02/11/2022 - The seminar is open to the public and registration is required each month. Dr. Hunter Mosely plans to discuss the richness of open data resources in biology and how they can support machine learning Read More...

02/12/2020 - This two-day instructor-led course gives participants a broad study of networking options on Google Cloud Platform. Through presentations, demonstrations, and hands-on labs, learners explore and deploy GCP networking technologies, such as Google Virtual Private Read More...

04/12/2019 - DNAnexus provides a secure cloud based platform for the analysis, storage and sharing of many different types of genomic data. CCR has recently established a Pilot program to enable CCR researchers to use this Read More...

04/11/2019 - DNAnexus provides a secure cloud based platform for the analysis, storage and sharing of many different types of genomic data. CCR has recently established a Pilot program to enable CCR researchers to use this Read More...

04/09/2019 - DNAnexus provides a secure cloud based platform for the analysis, storage and sharing of many different types of genomic data. CCR has recently established a Pilot program to enable CCR researchers to use this Read More...

06/26/2018 - DNAnexus provides a secure cloud based platform for the analysis, storage and sharing of many different types of genomic data. A point-and-click web environment provides ready access to powerful tools for the analysis, integration Read More...

05/16/2016 - This 2-day course, which includes both lecture and hands-on components, will teach the basic concepts and practical aspects of ChIP-Seq Data Analysis. There will also be a talk on ENCODE and a comprehensive discussion Read More...

02/19/2015 - This 2-day course, which includes both lecture and hands-on components, will teach the basic concepts and practical aspects of RNA-Seq Data Analysis. Learn everything from experimental design to statistical analysis. This workshop will include Read More...

11/18/2014 - Day 1 - AM (9:30-12:30)  Introductory Lecture ( Peter FitzGerald, PhD - CCR, NCI ) Introduction Historical Perspective and Technical Variations Experimental methodology Comparison to ChIP-Chip Data Analysis Experimental Design Quality Control  Peak Calling (Different methodologies) Major Read More...

06/16/2000 - We present the AMARETTO-Hub as a Knowledge Graph-based software platform that leverages Neo4j and Shiny to embed and interactively interrogate results generated by the *AMARETTO software toolbox that offers modular and complementary solutions Read More...

DNAnexus provides a secure cloud based platform for the analysis and sharing of next generation sequencing data. This resource allows simplified, secure access to the vast compute resources available via Amazon Web Services (AWS) and Read More...

Python is a programming language used in many different applications including data science. It is a high-level computer language, as the syntax is easily read and understood. Python is considered a beginner-friendly language. Python also Read More...

The Advanced Biomedical Computational Science (ABCS) group focuses on applications of bioinformatics, computational and data science, and artificial intelligence to support NCI researchers. ABCS provides: Subject matter expertise in genomics, proteomics, and imaging. Machine learning/ Read More...

The CLIA Molecular Diagnostics Laboratory (CMDL) provides an array of services for groups at the NIH Clinical Center, Fort Detrick, and Hood College, among others. They support cancer- and disease-related research by making Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Cores on CREx NIBIB BEPS Micro Analytical Immunochemistry Unit The Micro Analytical Immunochemistry Unit employs a variety Read More...

The Central Repository provides the research community at the NCI with various cryogenic services, including low-temperature storage from +4° C to -196° C, controlled-rate freezing, computerized inventory and distribution of samples. The Central Repository is operated Read More...

CREx News & Updates September 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Collaborative Research Exchange (CREx) News Site Spotlight FACILITY HIGLIGHTS Learn more about services from the CCR Read More...

The CCR Genomics Core is located in Building 41 on the NIH Bethesda campus. The primary goal of the Core is to provide investigators from CCR/NCI and other NIH Institutes access to genomic technologies and Read More...

The Mouse Metabolic Phenotyping Center (MMPC)Live Program provides standardized, high quality, unique, and hard to find phenotyping services for mouse models of diabetes, obesity, and related metabolic disorders. Emerging as the next iteration of Read More...

The Antibody Characterization Laboratory (ACL) is the laboratory responsible for the development of well-characterized monoclonal antibody reagents. The NCI’s Office of Cancer Clinical Proteomics Research funds ACL as a resource to the entire cancer Read More...

The Flow Cytometry Core (LGI) offers established technologies to support studies using flow cytometry and cell sorting. Established Technologies Applications that run on FACS Caliburs include: Immunophenotyping (up to 4-color), Intracellular markers, including cytokines and Read More...

The Genomics Laboratory (formerly Laboratory of Molecular Technology) is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, together with associated laboratory automation systems, data analysis, and information management Read More...

The CCR Collaborative Bioinformatics Resource (CCBR) is a centrally funded resource group which provides a mechanism for CCR researchers to obtain many different types of bioinformatics assistance to further their research goals. The group has Read More...

The Functional Genomics Laboratory (formerly, the RNAi Screening Facility) of the National Center for Advancing Translational Sciences (NCATS) assist investigators with all stages of project planning and execution, beginning with assay development through genome-wide siRNA Read More...

LCMB Microscopy Core offers live cell imaging technologies as well as super-resolution, fluorescence lifetime and confocal imaging systems for immunofluorescence. Our confocal instruments are a Leica SP8 laser scanning confocal microscope and a Nikon spinning Read More...

The Clinical Image Processing Service (CIPS) offers timely and accurate advanced image processing of diagnostic radiology images for clinical care, research, and training. CIPS’ functions include clinical services and scientific researches. Established Technologies: CIPS can Read More...

CLIA-Certified Technologies Offered: Fragment Analysis for Micro-satellite Instability Detection, Pharmacoscan Array for Pharmacogenomics, Mutation Detection for PCR and Sanger Sequencing, DNA extraction from whole blood, saliva, FFPE tissues, buccal swabs, nails, hair, PBMCs, buffy coats, Read More...

Back Services: Biophysics Facility offers Octet as an open-access instrument.  First-time users must complete a short training session before gaining access to the instrument reservation calendar.  Training includes a full analysis of a Read More...

The Genomics Technology Laboratory is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, data analysis, and information management tools, in support of CCR Investigators. The laboratory develops integrated Read More...

The Center for Advanced Preclinical Research (CAPR) specializes in evaluating the efficacy of preclinical compounds, existing drugs, or biologics (therapeutics) in genetically engineered mouse models, GEM-derived allograft (GDA) models, or patient-derived mouse xenografts (PDX). We Read More...

The NIH Center for Human Immunology, Inflammation, and Autoimmunity (CHI) is a trans-NIH resource whose mission is to provide a collaborative hub of advanced translational immunology for NIH clinical and pre-clinical studies. This uniquely structured Read More...

The AgingResearchBiobank was officially launched in January 2019 with a mission to provide a state-of-the-art inventory system for the storage, maintenance, and distribution of de-identified biospecimens and associated phenotypic, clinical, and imaging data from numerous NIA-funded Read More...

Back Services: Biophysics Facility offers MST as an open-access instrument.  First-time users must complete a short training session before gaining access to the instrument reservation calendar.  Training includes the KD determination of a Read More...

The Spatial Imaging Technology Resource (formerly the Nanoscale Protein Analysis Section of the Collaborative Protein Technology Resource or CPTR) provides expertise and service in state-of-the-art protein analysis technologies to advance CCR research in basic discovery Read More...

Services: Biophysics Facility offers CD as an open-access instrument.  First-time users must complete a short training session before gaining access to the instrument reservation calendar. Location: Building 50, room 3123 Description: CD spectroscopy measures the difference Read More...

Back Services: Biophysics Facility offers CD as an open-access instrument.  First-time users must complete a short training session before gaining access to the instrument reservation calendar. Location: Building 50, room 3123 Description: CD spectroscopy measures the Read More...

Home About the Biophysics Core Biophysics Core Services [tabby title="Instrumentation"] NHLBI Biophysics Core The Biophysics Core Facility: Overview Core Facilities provide scientific resources, cutting-edge technologies and novel approaches to support DIR scientists. Availability of Read More...

The facilities at AIM are available for use by the entire NIH intramural research community. While we welcome users with any size imaging project, AIM specializes in large, yearlong (or longer), collaborative research efforts with Read More...

The OSTR offers cutting-edge technology platforms to the CCR scientific community through centralized facilities. The videos accessed through this page are designed to introduce the various scientific methodologies OSTR makes available through the cores on Read More...

Learning Objectives This tutorial was designed to demonstrate common secondary analysis steps in a scRNA-Seq workflow. We will start with a merged Seurat Object with multiple data layers representing multiple samples. Throughout this tutorial we Read More...

This lesson provides an introduction to R in the context of single cell RNA-Seq analysis with Seurat. Learning Objectives Learn about options for analyzing your scRNA-Seq data. Learn about resources for learning R programming. Learn Read More...

Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To learn about options for report generation with R: RMarkdown and Quarto. Introducing Bioconductor Bioconductor is both an open source project Read More...

Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To generate high quality data reports using R Markdown to make data analysis more reproducible. Reminder: Uploading files from RStudio Server Read More...

Note This is not an exhaustive list. cBioPortal cBioPortal is a platform for exploratory and interactive visualization, analysis, and download of cancer genomics data. With cBioPortal You can quickly view genomic alterations across a set Read More...