![]() ![]() This preview will be maintained and updated when running a module or switching image sets. The Workspace Viewer from CellProfiler 2 has returned! This feature provides a customisable preview of your results during test mode, with the ability to overlay images, objects and measurements. This also grants access to all the 2D viewer tools when working with volumes. Normalization settings are applied across the entire volume. We’ve replaced this with a single-frame viewer accompanied by a slider to allow the user to view any plane in a volume. The 3D viewer added in CellProfiler 3.0 was somewhat limited. We’ve also added an option to apply display settings to all figures in the window, rather than needing to adjust each plot individually. The new contrast popup allows for brightness adjustment and changes to normalization with a live preview. We’ve revised the contrast display options when viewing figures. As a bonus, you can also use the arrow keys and ‘enter’ key to select and add modules from this dialog. Typing in the ‘Search modules’ box will now display a live list of modules with names matching the entered text. The ‘ Add modules’ dialog has been reworked to make finding modules faster. This new widget will also automatically highlight invalid selections. The “Add another image/object” buttons and dropdown lists have been replaced with a series of checkboxes to make selection easier. We’ve redesigned the interface for selecting multiple image and object sets in measurement modules. We’ve listened to your feedback and made adjustments to the user interface with the goal of making the software easier to use. It may be best to check these before running an upgraded pipeline.ĬellProfiler 4 has been far better-tested on successfully importing CellProfiler 3.X pipelines than on 2.1-2.3 pipelines if you encounter issues updating a CellProfiler 2.X pipeline into 4.0, consider importing first into CellProfiler 3, saving, then importing from 3 to 4.Īt its core, CellProfiler is built for scientists. Similar functionality can be achieved using the ExportToSpreadsheet module instead.Īs the pipeline encoding format has changed, text fields such as custom file list filters may not import correctly if they contain non-ASCII characters. The “MySQL/CSV” output mode from ExportToDatabase has been removed. Multiple copies of the module can be used to restrict measurements to specific images or objects. In upgraded pipelines this may result in extra measurements being recorded. The MeasureImageIntensity module now measures all selected images and objects together, rather than needing the user to specify individual pairs. Upgraded pipelines will attempt to analyse all images with the first set of parameters from the old pipeline ![]() Multiple copies of the module can be used to specify different parameters for specific images. The MeasureGranularity module now analyses all selected images with the same detection settings. The MeasureTexture module now allows users to explicitly select how many gray levels they wish to measure their images at- CellProfiler 2 used 8, CellProfiler 3 used 256. Users concerned about processing speed may wish to disable running Costes measurements in the module settings. This has now been corrected, but these statistics can be computationally expensive on high bit depth images. ![]() This could produce invalid results when working with 16-bit images. The MeasureColocalization module previously assumed that input images were in 8-bit format when performing Costes measurements. This can produce slightly different results. The MeasureObjectSizeShape module now uses the scikit-image implementation for most measurements. This will impact the Threshold, IdentifyPrimaryObjects and IdentifySecondaryObjects modules. In general, many of the libraries we use have updated their thresholding implementations, so thresholding settings on all upgraded pipelines should be checked and adjusted before use. The 3-Class Otsu thresholding method was calculated incorrectly in some situations and has now been fixed. Key points to take note of are as follows: This has involved extensive restructuring of the code base, leading to a lot of “under-the-hood” improvements.Īs a major release, this version contains changes to CellProfiler that will alter the behaviour of pipelines from previous versions of the software. The primary goal of this release has been to migrate CellProfiler from Python 2 to Python 3. We have now released CellProfiler version 4.0! Download it here. ![]()
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