This description suggests that CryoSPARC has been started with a blank database: no error, but also no contents . In this case, you may rebuild the database from scratch, as described in Cryosparc won't start after migrating the database to a new location - #9 by wtempel
Before doing this, you may want to upgrade CryoSPARC to the latest version and apply the latest patch for that version.
If the CryoSPARC installation remains at version 4.3.1, I strongly recommend ensuring that the file
/home/neher-lab/cryosparc/cryosparc_master/config.sh
includes the line
export CRYOSPARC_MONGO_EXTRA_FLAGS=" "
The space between the quotes is important. CryoSPARC needs to be restarted if the cryosparc_master/config.sh
is changed.