Community Service

New features:

• Plotting of gates in Session class: limited to polygon, rectangle, range, and ellipse gates.
• Session now supports importing FlowJo workspace files, though support is limited to WSP files with linear, log, logicle transforms, and only polygon & rectangle gates.
• Session class now supports multiple gating strategies via the implementation of "sample groups", similar to how FlowJo works.
• Sample class now allows retrieving events as Pandas DataFrames, with multi-index columns as the PnN and PnS labels

API changes:

• Session: add get methods for sample IDs, sample groups, and gate IDs
• More consistent handling of Matrix class as input to compensation methods
• Expose parse_gating_xml function
• Expose plot_channel function

Bug fixes:

• Handle case where a Sample has no keyword for original filename
• Fix re-subsampling after applying Sample filters
• Ensure correct fluoro order when parsing a comp matrix from a CSV file

Build Gates - 0.3.2

API changes:

• New Session method for adding samples after a Session instance has been created

Bug Fixes:

• Sample export failed to create file

Build Gates

New features:

• Programmatically add gates, transforms, and compensation matrices to a GatingStrategy
• Export a GatingML 2.0 compliant document from a GatingStrategy

API improvements:

• Gate sub-classes no longer require a GatingStrategy in their constructor, allowing re-use of instantiated gates
• New convenience methods in the Session class for getting parent gates and creating gates, transforms, and comp matrices
• Better x & y axis labels in scatter plot (includes marker names, if available)

Bug fixes:

• Fixed bug in GatingStrategy method get_gate_by_reference where an existing QuadrantGate could not be found
• Fixed bug in parsing spillover matrix from a $SPILL keyword value of an FCS file

In Session

Multiple API changes, significant performance improvements, and bug fixes for Windows.

• New GatingResults class for reporting gating statistics
• Significant performance improvements in calculating gated events
  • Support for multi-processing for evaluating gates
  • New C-extension for calculating events in PolygonGates
• Cleaner API for user interaction
• New Session class for combining multiple Samples with a GatingStrategy
• tSNE support for multiple Samples in a Session
• Automatic generation of a compensation matrix from a set of bead files
• Simplified API for exporting Sample events
• Multiple bug fixes for Windows

Gatin' 2: Electric Boogaloo

Now fully compliant with the GatingML 2.0 specification.

• Full support for GatingML Quadrant gate
• Now supports Ellipsoid gates of any dimension (not just simple 2-D ellipses)
• Sample class now takes any Transform sub-class, consistent with GatingStrategy transforms
• A new fancy logo!
• BUGFIX: fixed issue where the HyperlogTransform would fail on 2-D arrays

Hello, World!

1st release of FlowKit for flow cytometry analysis and visualization, featuring GatingML 2.0 support and support for reading and exporting FCS data