Version 1.0.5122 - New feature: Added checkbox to toggle image intensity scaling - Smooth: Changed 'Smooth' module to 'SmoothOrEnhance'and renamed 'RemoveBrightRoundSpeckles' to 'Tophat filter.' - Relate: Bug fix for segmented fields. - Align: Bug fix (minor). - CreateBatchFiles: properly change the "\" to"/" when modifying the paths for the images. Version 1.0.5019 - TrackObjects and Laplauccian of Gaussianwere added as modules. - TrackingTool added to the Data Tools. Version 1.0.4942 - MeasureObjectAreaShape:Zernike optimization: 30% - 50% reduced computation time. - MeasureImageSaturationBlur: added two more measurements: PercentMaximal and LocalFocusScore (actually NormVar of Local NormVariances). - CPthreshold, IdentifyPrimAutomatic,IdentifySecondary,MeasureImageAreaOccupied:Added Kapur entropy-based threshold method and added two thresholding quality metrics. - CPthreshold, IdentifyPrimAutomatic:Adjusted MoG to give precisely the same answer each time by setting rand seed to zero. - CellProfiler.m:added a check to make sure the directory exists when user tries to open a file from the file listbox in the main window. - Relate: Bug fix: Fixes exporting problem when no parents are found. Now initializes every handles.Measurements.(SubObjectName).Distance to have at least one zero, which was causing problems when exporting. Also added clarification to a warning dialog. - CPrelateobjects: add features even when objects are missing. - CPthreshold: Bugfix: a couple wv -> soe in SumOfEntropies subfunction. - ClassifyObjects: Two bug fixes: (1) Now guards against Inf's in lower or upper Bin bounds, and (2) colormap is now correctly set for data ranges smaller than the default colormap (plots for were blank previously). - MaskImage: now a figure window is displayed. Version 1.0.4884 -New distance measurement in the Relate module. -Updated LoadImages module to handle more movie files. -New DataTool for CalculateStatistics. -Optimized Zernike calculations optimization by 30-50% less computational time. Version 1.0.4828 -Created Stack for troubleshooting problems in the error messages. -Fixed "*/.mat" in openning files. -Normalized Zernike measurements by area. -CPSmooth and related smoothing modules (IdentifyPrimAutomatic and Smooth)--fixed median filtering to be median. Added Gaussian filtering. -CellProfiler optimization in MeasureObjectIntensity. -Removed 'Pack' as an option in CellProfiler. Pack will only work in commandline. Version 1.0.4684 - Fixed bug for loading a pipeline from a previous version Version 1.0.4666 - CalculateStatistics.m - an error in calculating Z'-factors was fixed. Previously, Z'-factors were calculated from the most extreme effects, rather than the most extreme doses. - Windows-32bit version: MEX file error in the IdentifyPrimAutomatic module has been fixed. Version 1.0.4628 - FilterByObjectMeasurement does not fail when using texture measurements - ClassifyObjects includes image name in output to distinguish different modules - ConvertToImage has option to save in uint16 format - CalculateStatistics now returns 0 for invalid EC50, instead of crashing Version 1.0.4553 - GenePix format TIF files are now supported - MeasureImageGranularity now correctly stores granularity data - IdentifySecondary and FilterByObjectMeasurement now export locations of [0 0] when there are no initial objects - Fixed bug with MeasureTexture not being able to measure 'Image' correctly Version 1.0.4532 - CalculateStatistics now returns correct results with only 1 data point (image) per dose - SaveImages can now automatically number images when there are more then 100 cycles - Several various bug fixes Version 1.0.4303 - Added MeasureImageSlope and Combine modules - Histogram data tool overhauled - New thresholding options in IdentifyPrimAutomatic - Updated FindEdges Module - ZVI file format is now supported - Many feature names have been shortened to ease transition in to database Version 1.0.3775 - Windows menu now shows all CellProfiler windows - Added module MaskImage - Changed smoothing method to use gaussian filter instead of binary - MeasureTexture uses ScaleOfTexture for objects - MeasureObjectNeighbors records closest 2 objects and their vectors and percent of neighbors touching each object - ExportToDatabase creates MySQL tables with FLOAT NOT NULL to improve speed - ExportData can export labels created by ClassifyObjects - Added help menu for Modules - Several various bug fixes Version 1.0.3544 - Added new help section "Getting Started" - Added help on Batch Processing - CreateBatchScripts is now CreateBatchFiles - CreateBatchFiles can produce files for CPCluster, which allows users to do cluster analysis without MatLab licenses - WriteSQLFiles is now ExportToDatabase - ExportToDatabase can export SQL files for MySQL and Oracle - ShowDataOnImage can now show text labels added with LoadText or AddData - ClassifyObjects can now label bins, which can be seen with ShowDataOnImage Version 1.0.3443 - Added meander mode for tiling images - Rotate correctly states that a positive angle gives counterclockwise rotation - MergeBatchOutput now looks in Default Output Folder - Timer functionality is improved - Added ExportToExcel module (same function as ExportData) - WriteSQLFiles now creates a correct SQL file to setup and import all CSV files - LoadImages and LoadSingleImage always display correct filenames - Pipelines should no longer become corrupt. If the error occurs, a warning tells the user to report to mrl@wi.mit.edu - Several various bug fixes Version 1.0.3215 - ClassifyObjects can now handle no objects - MeasureCorrelation white background has been changed to CP colors - CPhistbins can now handle data sets with zeroes Version 1.0.4818 - Smoothing has been updated. Previously, 'median filtering' was really 'Gaussian filtering.' We have added Gaussian Filtering and fixed Median Filtering. To achieve similar results, you will need to use the 'Gaussian Filter' setting. Modules where you may notice this change: CorrectIllumination_Calculate, CPSmooth, IdentifyPrimAutomatic, and FindEdges. - CPSmooth speed optimization. - Fixed */.mat bug when selecting or saving a pipeline. - Normalized Zernike measurements by area. Version 1.0.4828 - Added distance measurement to be calculated when using the Relate module (and fixed several related bugs). - Fixed wait bar color issue - Removed 'Pack' as an option in SpeedUpCellProfiler Version 1.0.4884 - Modified Z factors,V factors,CPec50 to be used by the CalcuateStatistics Data Tool. - Memory usage now reported in the 'Details'window. - PauseCellProfiler module is released. - GroupMovieFrames module is released for grouping specific frames of movie files. - Relate module changes: (1) Minimum distances between Child and Parent are now calculated, (2) a second Parent object can be defined ('Other Object'), (3) and if so, normalized distances are also calculated, (4) some sanity checks on these new settings. - LoadImages changes: add a capability to load tif,tiff,flex multi-page files. Version 1.0.4942 - Fixed minor bugs in exporting data after using the Relate module. - Allow user to save the image created from MeasureImageAreaOccupied. - Display window for MaskImage module. - Released new modules: KeepLargestObject and UnifyObjects.