New CellProfiler Analyst release

A new version of CellProfiler Analyst has been released and is available for download for PC and Mac at

Windows users: We’ve noticed that on some machines running CPA for the first time may take a very long time to start up. We’ve found this to be caused by antivirus software. You have 2 options to get around this.

  1. Configure your antivirus software to whitelist CPA.
  2. Wait. And wait. After the first run, your antivirus software should recognize CPA and it should start up quickly.

The new release includes some bugfixes as usual and the following:

  • 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



great work! thanks!

however, when i start it on a Win32 machine i get the message: “Is not a valid Win32 Application”.
is that true or do i do something wrong?

cheers, tischi

Note: there will be a re-release to address the Win32 issue and one with Bioformats.

Please see: CPA re-release coming soon for more details.

CPA r11306 has been released and addresses the issues mentioned above. Download it here.