H5CellProfiler

Data analysis and graphics package* with a browser based GUI. Functions as interface for the HDF5-format output from the open source image-analysis tool CellProfiler.

Described in more detail in:

Wink, S., Burger, G. A., Le Dévédec, S. E., Beltman, J. B., & van de Water, B. (2022). User-friendly high-content imaging analysis on a single desktop: R package H5CellProfiler. bioRxiv. https://doi.org/10.1101/2022.10.06.511212

*Note: not installable/ packageable yet

H5CellProfiler bat versions (Windows only)

Adding pandoc to PATH

You need to add pandoc to your PATH. First start RStudio and execute

Sys.getenv('RSTUDIO_PANDOC')

You should follow the instructions here to add an environment variable. The variable should be PATH (or Path )

• If that variable already exists, add a ; (semicolon) at the end plus the directory you get from the above command, but without pandoc.exe (most likely C:/Program Files/RStudio/bin/pandoc). (In Windows 10 you can also double click the Path entry and then just past the directory in a new row)
• If it doesn't exist you should create it

Adding powershell to PATH (only if it complains about not being able to find it)

Most likely powershell is at C:\Windows\System32\WindowsPowerShell\v1.0 so go there to check if that is indeed the case, and append it to your Path environment variable using the instructions above