Probability Map Viewer Collection mode with DM4 files

Probability Map Viewer also supports collection mode with DM4 files using IMOD to do the conversion.

Follow the instructions on Probability Map Viewer in collection mode, but make the following changes:

• IMOD is needed to convert the DM4. See Installing IMOD for instructions.
• Skip the creation of the slice_### directory.
• Skip download of example.png and convert command.
• Replace --collectionmode flag with --dm4collectionmode
• The .dm4 files should be put under collection/ directory
• chmutil needs to be installed on machine to assist in dm4 file conversion

Probability Map Viewer will look for the 2nd newest DM4 file and convert it to tiles and store in them in slice_### directories.

The reason for 2nd is based on the premise that if a newer DM4 file is being written, the previous one has been completely written to disk.

Other flags specific to DM4 collection mode

• --downsamplefactor Tells Probability Map Viewer how much to downsample the DM4 before conversion to tiles. Default is 4.

• --dm2mrcbinary Sets path to dm2mrc binary. Default is dm2mrc.

• --mrc2tifbinary Sets path to mrc2tif binary. Default is mrc2tif.