CellProfiler is designed for biologists without training in computer vision or programming to quantitatively measure cells in thousands of images automatically. It has a user-friendly graphical interface. CellProfiler has a modular, flexible infrastructure which allows you to conveniently conduct a series of image analysis steps on thousands of images. While designed for biology applications, it can find any objects in images given the right adjustments to settings. It especially handles grids of spots well. It also can handle file-processing tasks like creating montages of images, renaming files, and creating web pages of images. It is easy to write new modules in Matlab.

MATLAB_CellProfilerv1.0
.......................\CellProfiler.m
.......................\CPsubfunctions
.......................\..............\CPaddmeasurements.m
.......................\..............\CPaverageimages.m
.......................\..............\CPcd.m
.......................\..............\CPclearborder.m
.......................\..............\CPcompilesubfunction.m
.......................\..............\CPcontrolhistogram.m
.......................\..............\CPconvertsql.m
.......................\..............\CPdilatebinaryobjects.m
.......................\..............\CPerrordlg.m
.......................\..............\CPfigure.m
.......................\..............\CPgetfeature.m
.......................\..............\CPhelpdlg.m
.......................\..............\CPhistbins.m
.......................\..............\CPimagesc.m
.......................\..............\CPimagetool.m
.......................\..............\CPimread.m
.......................\..............\CPlabel2rgb.m
.......................\..............\CPlogo.m
.......................\..............\CPmakegrid.m
.......................\..............\CPmsgbox.m
.......................\..............\CPnanmean.m
.......................\..............\CPnanstd.m
.......................\..............\CPplotmeasurement.m
.......................\..............\CPquestdlg.m
.......................\..............\CPrelateobjects.m
.......................\..............\CPrescale.m
.......................\..............\CPresizefigure.m
.......................\..............\CPretrieveimage.m
.......................\..............\CPretrievemediafilenames.m
.......................\..............\CPrgsmartdilate.m
.......................\..............\CPsmooth.m

.......................\..............\CPtextdisplaybox.m
.......................\..............\CPtextpipe.m
.......................\..............\CPthreshold.m
.......................\..............\CPthresh_tool.m
.......................\..............\CPwaitbar.m
.......................\..............\CPwarndlg.m
.......................\..............\CPwhichmodule.m
.......................\DataTools
.......................\.........\AddData.m
.......................\.........\ClearData.m
.......................\.........\ConvertBatchFiles.m
.......................\.........\DataLayout.m
.......................\.........\ExportData.m
.......................\.........\ExportDatabase.m
.......................\.........\ExportLocations.m
.......................\.........\GenerateHistogramMovie.m
.......................\.........\Histogram.m
.......................\.........\MeasurementCalculator.m
.......................\.........\MergeOutputFiles.m
.......................\.........\PlotMeasurement.m
.......................\.........\ShowDataOnImage.m
.......................\.........\ViewData.m
.......................\Help
.......................\....\HelpColormaps.m
.......................\....\HelpCPInstallGuide.m
.......................\....\HelpDefaultImageFolder.m
.......................\....\HelpDefaultOutputFolder.m
.......................\....\HelpFastMode.m
.......................\....\HelpGettingStarted.m
.......................\....\HelpMatlabCrash.m
.......................\....\HelpOutputFilename.m
.......................\....\HelpPixelSize.m
.......................\....\HelpPreferences.m
.......................\....\HelpProgrammingNotes.m
.......................\....\HelpSkipErrors.m
.......................\....\HelpTechDiagnosis.m
.......................\ImageTools
.......................\..........\ImageToolWindow.m
.......................\..........\InteractiveZoom.m
.......................\..........\OpenNewImageFile.m
.......................\..........\ShowOrHidePixelData.m
.......................\MATLAB_Install.txt
.......................\Modules
.......................\.......\Align.m
.......................\.......\ApplyThreshold.m
.......................\.......\Average.m
.......................\.......\CalculateRatios.m
.......................\.....

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