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Getting Started
About Cytobank
Account Basics
Security
Cytobank Essentials: Core Overviews
Cytobank Core Overview Articles
- Overview of uploading data to Cytobank
- Overview of Cytobank anatomy and organization, basic concepts
- Overview of the Inbox
- Overview of Gating in Cytobank
- Overview of Sample Tags: annotating scientific and experimental variables in Cytobank
- Overview of Figure Generation using the Working Illustration
Gating
Articles on Gating
- Overview of Gating in Cytobank
- The Difference Between a Gate and a Population: Using the Population Manager and considerations for deleting and renaming gates
- Hidden gates: a gate is tied to a compensation, channel selection, and scale settings, and is visible only when they are set accordingly
- The "Apply" and "Apply and Return" buttons and gate versioning
- Seeing Gate Location Across All Files in the Experiment (Check Gates functionality)
- Tailoring the location of a gate to files and populations
Gating-based Visualizations
Sample Tags and Annotating Scientific Variables
Articles
- How to Annotate data with Sample Tags in Cytobank (tutorial)
- Annotate data during collection for efficient transfer to Sample Tags in Cytobank
- Import Sample Tags from an existing Cytobank Experiment
- Exporting and importing Sample Tags: annotate files by spreadsheet
- Apply Sample Tags Based on Custom Metadata Fields Within FCS Files
- The Plate Annotation Tool
Panels, Channels, and File Categorizations
Figures (Illustrations)
Articles
- Using the Layout Placeholders tab
- Understanding the Working Illustration and Saved Illustrations
- Download or Export Plots and Figures as Images, SVG, PDF, or to PowerPoint
- How to create and configure a Heatmap
- Statistics and fold change equations in the Working Illustration
- How to export and download statistics from an Illustration
Advanced Analysis - SPADE, viSNE, and CITRUS
Articles on SPADE
- Overview and introduction to SPADE
- How to Configure and Run a SPADE Analysis
- SPADE with fold change: overview, setup, and analysis
- Analysis and Interpretation of SPADE Results
- SPADE metrics: Median, Raw Median, Fold, Raw Fold, and CV
- Export images of a SPADE tree
Articles on viSNE
- Introduction to viSNE in Cytobank
- How to Configure and Run a viSNE Analysis
- Analysis and Interpretation of viSNE Results
- How to Concatenate viSNE files for Analysis
- SPADE on viSNE: Automatically Categorize viSNE Populations
- viSNE FAQ
Articles on CITRUS
Data Scaling and Transformation
Articles
Compensation
Articles on Compensation
- Import a compensation matrix from a CSV file into Cytobank
- Working in Cytobank with data compensated in a different software
- Create a compensation matrix automatically from single stain controls (automatic compensation)
- Import an existing compensation matrix from another Cytobank experiment
- Modify a file-internal compensation matrix in Cytobank (import a compensation matrix from an FCS file)
- Create or modify a compensation matrix manually
Exporting Data and Statistics
Articles on Exports
- Important notes on the Percent in Gate statistic
- Export data as FCS or spreadsheet files from whole files and/or gated populations
- Download FCS files and other files from Cytobank
- Download and transfer an entire Experiment and analyses between Cytobanks as an ACS file
- Exporting a spreadsheet of batched statistics using the Export Statistics Tool (for import into Prism, Spotfire, Excel, Tableau, etc.)
Data Management, Sharing, Collaboration, and Permissions
Articles on Data Sharing
Articles on Data Management
- Upload fresh data to Cytobank
- Clone an experiment to make a copy for your own use
- The Experiment Summary page
- The FCS file details page
- Warnings on FCS files: Understanding the Cytobank File QC system
- Delete an experiment
Publishing on Cytobank
FAQ
The Cytobank API
Articles on the Cytobank API
Templated Analysis
Analysis Templates Articles
- Compensation templates
- Statistics export templates
- Illustration/figure settings templates
- Illustration/figure templates: transfer saved illustrations between Experiments (import illustrations)
- Sample Tags templates
- Gating templates
Misc
Articles
- How to reference Cytobank when publishing
- How to open and use your browser's JavaScript console
- How to analyze gene expression or imaging data in Cytobank (CSV to FCS)
- Using keyboard hotkeys
- Adjust the default view of the Inbox
- Titrations in Cytobank