vorticowboy.blogg.se - Assertionerror cellprofiler threeshold

#ASSERTIONERROR CELLPROFILER THREESHOLD UPDATE#
#ASSERTIONERROR CELLPROFILER THREESHOLD CODE#
#ASSERTIONERROR CELLPROFILER THREESHOLD WINDOWS#

#ASSERTIONERROR CELLPROFILER THREESHOLD CODE#

The option is present in 2.1.0, but IdentifyPrimaryObjects had no code to join small objects and behavior was the same whether or not the option was selected. The option to join small objects has been removed from IdentifyPrimaryObjects.Semi-pointless tooltip removed from module settings panel (issue #1065).Old pipelines will fill holes both after thresholding and segmentation. The user can choose to never fill holes, to fill holes only in the final segmentation or fill holes both after thresholding and segmentation.FillHoles is designed to fill holes within objects so it’s inappropriate to fill a hole that is larger than any potential object that could contain that hole. The FillHoles option will not fill holes larger than the maximum cell diameter, squared.FillHoles now fills holes that would have not otherwise been filled, for instance if you have a confluent field of cells, all holes in the thresholded image would be filled by the corrected version. IdentifyPrimaryObjects – (Issue # 1133) IdentifyPrimaryObjects fills holes twice – once after thresholding and once after separating touching objects.IdentifyPrimaryObjects / IdentifySecondaryObjects – Do not smooth the image when thresholding by a measurement or using manual-mode.The former calculation is preserved as “Log Transform (legacy)” and all old pipelines use that instead of the new log-transform calculation. ImageMath: The log-transform option now performs log2(x+1) which transforms the range, 0-1, to the range 0-1.

The ClassifyPixels module is loaded on platforms that do not support it, but it displays an error status.Similarly File / Export / Pipeline appends “.cppipe” (issue #918) On OS/X, “.cpproj” is appended to the file name entered in File / Save Project As unless the filename already ends in “.cpproj”.Use “-p” for both pipelines and projects – CellProfiler will figure out what to do based on file type. The default choice for file output location for ExportToSpreadsheet and UntangleWorms has been changed to the default output folder to match the behavior of ExportToDatabase, SaveImages, CreateBatchFiles and MeasureNeurons (issue #1070).Better error messages if matching by order and NamesAndTypes finds more images in one channel than another (Issue #714).csv file has more fields than there are headers, ignore the extra fields instead of preventing the user from using the file (issue #853) csv file along with a setting that lets you disable the warning and silently overwrite the. Added a warning dialog that is displayed if your pipeline tries to overwrite a.Issue #1004 – added a setting that asks you if you want to use an HTTP prepend (previously, you’d leave the text blank to indicate that).

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Issue #1003 – warn user if SQLite is used with the CreateBatchFiles module (you can’t update a SQLite database that’s open in another process).

Issue #1105 – added a keyboard shortcut to toggle between showing objects as outlines or using an alpha-blend of the image and colored object.

Issue #1054 – added a button that toggles outlines off and on.

Added setting that allows user to create an output image of just the numeric data on a black background (issue #978).

Added a preference to optionally save the pipeline and / or file list when saving a project (Issue #1160).

#ASSERTIONERROR CELLPROFILER THREESHOLD WINDOWS#

Show the group number and index of the image set within the group in the title of module display windows for pipelines that use grouping.

The “-o” command-line switch will create the indicated output folder if it doesn’t exist (Issue 1025).

If a module is marked as “paused” for test mode and the project or pipeline is saved and reloaded, the module remains marked as “paused” on loading.

Use the color-picker setting to pick colors in OverlayOutlines, DisplayDataOnImage and ExportToDatabase.

Added an “-omero-credentials” command-line switch to let CellProfiler authenticate with Omero in headless mode (issue #1052).Added ctrl-p shortcut to save the current pipeline to a file.Added a preference that controls the default maximum Java heap size (Issue #787).Better error messages if File -> Open Recent and other try to open a non-existent file (Issue #668).Improved display of notifications when user tries to analyze images, but the project configuration does not produce any image sets (Issue #1055).Issue numbers cited below correspond to those on Github ( ). For brief overviews of each release, see the CellProfiler release notes. This page contains a very detailed list of bugs fixed in each version. This page is now deprecated, future release notes can be found on the releases page and the blog.