CPA re-release (r11306)

CellProfiler Analyst r11306 is available for download for PC and Mac at cellprofiler.org/downloadCPA.shtml

This release is meant to replace r11246 which wasn’t properly built for win32, and which accidentally had the Bioformats image loader turned off.

As with 11246, this release includes:

  • Bioformats
    is now used for reading images, this means support

  • Plate annotation tools
    added to PlateViewer. This allows the user to annotate their plates manually by clicking on wells and typing in labels or values which are stored automatically in a new user defined column in the per-image table.

  • Gates can be created and modified from within the Scatterplot, Histogram, and Density plot. A Gate is essentially a 1D or 2D selection that constrains 1 or 2 measurements to a particular interval. This simple construct is very useful for establishing acceptable ranges for quality control.

  • Gates can be used as filters in nearly all the places that filters are available.

  • Gates can be used to create a table of acceptable images which you can then save as a CSV and load with CellProfiler LoadImages.

  • Images and objects within a given gate can be shown by drawing or selecting a gate from one of the plots, then right-clicking and selection “Show images/objects in gate”

  • Filters (and gates) can now be applied when viewing data in PlateViewer.

  • "Show objects from selection"
    option added to scatterplot.

  • Added a SQL query maker tool
    available from the Advanced menu.

  • Added normalization tool
    available from the Advanced menu.

  • Properties can now be saved
    so you can retrieve Filters and Gates created during a session.

  • Users can now create multiple boxplots from a single column by selecting a grouping.

  • Scatter plot & density plot can now plot data from different tables on each axis.

  • CPA now starts up significantly faster when filters are defined in the properties file.

  • Workspaces now store zoom/pan coordinates of each plot.

  • Developers: CPA now only requires MySQLdb to be installed if you are connecting to a mysql database. Same for SQLite3.

  • Per-Object table is no longer required for many tools.

  • UI is less ugly on Windows.

  • Bugfix: When image thumbnails were present: If you start PlateViewer and change the plate, then right-click on a well to show the combined thumbnail, you still see the thumbnail for that well but from the original plate (i.e., the selected one on startup), not the current one.

  • Bugfix: CPA crashed after dismissing a thumbnail montage and clicking on another well.

  • Bugfix: Boxplot handles nulls

  • Bugfix: Selecting particular images to display in PlateViewer was always showing the last image from the site.

  • bugfix: Selection in Scatterplot was broken when nulls were plotted

Enjoy!