z_position_tracker

This function tracks the z position of the 2p imaging plane frame by frame, using a reference z-stack file. The original function was created by Rich Hakim in 2023.

How to run the code

1. Modify the following lines of code to make it work on your local system.

• /n/data1/hms/neurobio/sabatini/gyu/github_clone/z_position_tracker/cmd_single_process.sh
  • Line 3, #SBATCH --output=YOUR SLURM_OUT PATH
  • Line 12-14, Match module version to your system
  • Line 16, Activate your environment
  • Line 18, cd to your z_position_tracker dir
• /n/data1/hms/neurobio/sabatini/gyu/github_clone/z_position_tracker/cmd_z_tracking.sh
  • Line 3, #SBATCH --output=YOUR SLURM_OUT PATH
  • Line 11-12, Match module version to your system
  • Line 14, Activate your environment
  • Line 16, cd to your z_position_tracker dir
• /n/data1/hms/neurobio/sabatini/gyu/github_clone/z_position_tracker/slurm_z_tracking.py
  • Line 27, Change the default path_params
  • Line 318, Change the default path_params

2. Carefully double-check your params.yml file.

3. You are now ready to run z-tracking by entering just one command-line input!

• Default: sbatch /n/data1/hms/neurobio/sabatini/gyu/github_clone/z_position_tracker/cmd_z_tracking.sh
• You can change the slurm output directory by entering: sbatch --output=YOUR_SLURM_OUT_DIR /n/data1/hms/neurobio/sabatini/gyu/github_clone/z_position_tracker/cmd_z_tracking.sh
• You can also input directories in the command-line input. The command-line input will overwrite the params.yml input.
  • Example: sbatch /n/data1/hms/neurobio/sabatini/gyu/github_clone/z_position_tracker/cmd_z_tracking.sh --dir-video-exp /n/data1/hms/neurobio/sabatini/gyu/github_clone/z_position_tracker/tester/exp

Unresolved Error

• There seems to be an unexpected / unresolved error with ScanImageTiffReader when it is called on non-interactive slurm node.
  • Quick-and-dirty makeshift: Comment out Line 309-310 of init.py in ScanImageTiffReader
  • Comment-out Lines:
    • if self.__ctx.log:
    • raise Exception(self.__ctx.log.decode("utf-8","strict"))