![]() The LoadData module uses the first row of the file as a header. Text values may be optionally enclosed by double quotes. The lines of the file represent the rows, and each field in a row is separated by a comma. These files can be produced by saving a spreadsheet from Excel as "Windows Comma Separated Values" file format. The module currently reads files in CSV (comma-separated values) format. However, old pipelines loaded into CellProfiler that contain this module will provide the option of preserving them these pipelines will operate exactly as before. This module loads a file that supplies text or numerical data associated with the images to be processed, e.g., sample names, plate names, well identifiers, or even a list of image filenames to be processed in the analysis run.ĭisclaimer: Please note that the Input modues (i.e., Images, Metadata, NamesAndTypes and Groups) largely supercedes this module. We’re working to try to correct this problem in future versions of CellProfiler.Load Data loads text or numerical data to be associated with images, and can also load images specified by file names. These last two errors are particularly sneaky: if you hover over a dropdown menu with a scroll-wheel mouse, you can accidentally scroll down to a different option, messing up a configuration that was previously correct. ![]() You’ve used ‘Metadata’ for your Image set matching rather than ‘Order’, but you haven’t set it up correctly.You’ve told it to use ‘Directory does contain ‘ch3’’ to define your DNA image, but you meant to set it to ‘File does contain ‘ch3’’.You’ve told it to set files containing ‘ch4’ as your DNA image but your experiment only has files ending in ‘ch1’, ‘ch2’, and ’ch3’.One of the sets of rules you’ve used to identify a channel isn’t set correctly – for example:.You turned on ‘Groups’ but never gave it a piece of metadata to group by (in which case the ‘Metadata category’ is still set to ‘None’).Check the output of the Metadata module to ensure all of your images have the information that they need. A piece of extracted metadata is missing (e.g., you remembered to extract the Plate metadata from your ‘regular’ images but not from your illumination correction functions).You forgot to hit ‘Update’ in the Metadata module when using the ‘Extract from image file headers’ option.Your image files have been moved to a different location on your computer, but CellProfiler is still looking for them in their original location.But here are some common triggers for this kind of error. If you want to learn more, we recommend reading the help sections for each module, and everything under ‘Help->Creating A Project’ is a fantastic resource as well (we’ve included a table from it below that’s a great cheat sheet to understanding these modules). These errors simply mean that CellProfiler doesn’t know how to sort the images you’ve given it, and it can’t process them until it knows how they should be organized. If you have mistakes in any of these modules, you may run across the dreaded errors ‘The pipeline did not identify any image sets’ or ‘Sorry, your pipeline doesn’t produce any valid image sets as currently configured’. But it’s sometimes confusing what each one does, and it’s not always obvious which ones you need for your experiment. Incoming images are configured in the first 4 modules of CellProfiler – Images, Metadata, NamesAndTypes, and Groups – which offer lots of flexibility. Defining the input to CellProfiler can be the hardest part of getting your pipeline set up and your analysis underway.
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