Table 1 ∣.

Troubleshooting table

Step	Problem	Possible reason	Solution
1	Cannot run the segmentation pipeline: the pipeline did not identify any image sets	The user did not load any images in the “Images” module	Drag and drop images into the “Images” module of CellProfiler
	Subfolder under CellProfiler output folder is named “None”	The metadata extraction rule is incorrect	Modify the extraction rule under the “Metadata” module in CellProfiler
4	A warning is given that the MATPLOTLIBDATA environment variable is deprecated in Matplotlib 3.1 and will be removed in 3.3	The executable file of VAMPIRE is created using software that uses a variable that will be removed in the future	Ignore this message since VAMPIRE is not affected by this warning
10	The following warning appears: “IndexError: arrays used as indices must be an integer”	Segmented images do not contain any cell or nucleus	Check if segmented images have a correct format as specified in Step 2 and that they have at least one cell or nucleus
	The following warning appears: “RuntimeWarning: Mean of empty slice”	The number of objects is less than the number of clusters	Provide images with a greater number of cells than the number of clusters
	The following warning appears: “Permission denied”	CSV file is open while the analysis is running	Close all open CSV files and repeat Step 10