Welcome to the Cytobank Support Portal!
Use the search bar below to locate articles, or scroll downward to browse categories.
Support requests can be submitted using the link in the upper right.
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
Panels, Channels, and File Categorizations
Figures (Illustrations)
Articles
- Using the Layout Placeholders tab
- Understanding the Working Illustration and Saved Illustrations
- The various ways to download or export plots and figures as images, PDFs, 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 choose a population for SPADE
- How to choose clustering channels for SPADE
- How to choose a target number of nodes/clusters for SPADE
- Density-dependent downsampling and SPADE
- The effect of scale settings on SPADE results
Articles on viSNE
- Introduction to viSNE in Cytobank
- How to choose channels for viSNE
- viSNE sub-experiments and running viSNE or SPADE on the results of a viSNE run
- viSNE separates files by population...how to recombine viSNE files for analysis
- The effect of scale settings on viSNE results
- Does viSNE downsample or upsample the data during analysis?
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 text 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
- All the ways to share data on Cytobank
- Give another Cytobank subscriber full access to an experiment
- Use projects to share data, collaborate with a group, and set custom access permissions
- Sharing with Cytobank subscribers across different Cytobanks
- The Experiment Summary page
- The FCS file details page
Getting Data Onto Cytobank
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