![]() ![]() Compensation controls (single stain samples) must now belong to a compensation group in order to create a compensation matrix with these controls. 2020, doi:10.26508/lsa.Chapter 2 – Creating a New Compensation Matrix in FlowJo CHAPTER 2 – Creating a FlowJo compensation matrix from single stain controlsīefore compensating data in FlowJo, be sure your parameters which require compensation are scaled correctly.Ĭompensation has been reworked for version 10. "Profiling of immune dysfunction in COVID-19 patients allows early prediction of disease progression." Life science alliance vol. “Combining real-time fluorescence spectroscopy and flow cytometry to reveal new insights in DOC and cell characterization of drinking water.” Frontiers in Environmental Chemistry (2022), doi:10.3389/fenvc.2022.931067 If you have a package or publication where FlowKit was used, and you want it listed here, feel free to submit an issue letting me know. The following projects and publications have utilized FlowKit. FlowKit: A Python toolkit for integrated manual and automated cytometry analysis workflows. White, S., Quinn, J., Enzor, J., Staats, J., Mosier, S. Read our CONTRIBUTING guidelines Cite FlowKit Want to get involved in the development of FlowKit? Saving Flow Analysis Data as AnnData objects for ScanPy.Comparison between Leiden & Louvain clustering.Dimension reduction on gated populations.Importing a FlowJo 10 WSP file & replicating analysis in FlowKit.Compare mean fluorescence intensity (MFI) in gated populations.If you have an example you would like to submit for consideration in this list (preferably with data), please submit an issue. Part 3 - GatingStrategy & GatingResults Classesīelow are more advanced and practical examples for using FlowKit.Part 2 - transforms Module & Matrix Class.Or, clone the repo and run them locally to see the fully interactive plots. The rendered versions are available on our documentation page here. Note, the interactive scatterplots do not render on GitHub. ![]() The series of Jupyter notebook tutorials can be found in the docs/notebooks directory of this repository. ChangelogsĬhangelogs for versions are available here Tutorials If you have any questions about FlowKit, find any bugs, or feel something is missing from the tutorials below please submit an issue to the GitHub repository here. The tutorial notebooks in the docs/notebooks directory are a great place to get started with FlowKit, and are linked below. The FlowKit API documentation is available on ReadTheDocs here. NOTE: For macOS users running on Apple Silicon, the version of pip may need to be upgraded prior to installing FlowKit in order to install the required dependencies. If compiling using gcc, version 5 or later is required. NumPy >=1.19 must be installed prior to compiling FlowUtils. If a pre-built binary of FlowUtils is not available for your environment, the C extensions must be compiled using the source package. For most platforms and Python versions, pre-built binaries are available in PyPI (i.e. NOTE: FlowUtils uses C extensions for significant performance improvements. Interactive scatter plots of gates with sample eventsįlowKit supports Python version 3.7 - 3.10.Interactive scatter plot matrix of any combination of channels.Interactive scatter plot of two channels.Retrieve gating results as a Pandas DataFrame.Programmatically create gating strategies including polygon, rectangle, range, ellipsoid, quadrant, and boolean gates.Polygon, rectangle, ellipse, and quadrant gates.Linear, logarithmic, bi-exponential, and logicle transforms.Import FlowJo 10 workspace files, supporting the following features:.Export gating strategies as a valid GatingML XML document.Import GatingML XML documents as gating strategies.Full support for the GatingML 2.0 specification.GatingML 2.0 spectrumMatrix XML element.Compensate events using spillover matrices from:.Read FCS files, supporting FCS versions 2.0, 3.0, and 3.1.FlowKit is a Python toolkit for flow cytometry analysis and visualization, with full support for the GatingML 2.0 standard and limited support for FlowJo 10 workspace files. ![]()
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