BRAIN CoGS mini VR rigs

# Ephys/Imaging Automation Pipeline

# Initial configuration

  • Note: These steps are only needed if a label in red with "Configuration needed" is shown on the top right corner of the GUI.
Configuration needed label
Configuration screen
  1. Switch to "System Configuration" tab.
  2. Click "Start Configuration" button.
  3. In "System Name" dropdown, select corresponding system (normally named room#-Recording#).
  4. In "Associated Behavior Rig" dropdown, select corresponding rig paired with recording system.
  5. Click "Add Rig to System" button.
  6. Repeat steps 4 & 5 until all rigs associated to recording system are added.
  7. In "Recording Modality" dropdown select corresponsing modality of the recording system.
  8. In "Recording Root Folder" area, click folder button to search for Parent path where all recordings will be stored.
  9. Click "Configure System" button.
System configured correctly

If something was configured incorrectly, you can repeat the whole process.

# Automation GUI "regular use" Manual

  • The automation GUI is located on the desktop in all microscope/ephys recording system across BRAINCoGS. You can identify it by a desktop BRAINCoGS icon called "Recording_Automation_GUI".
  • It is encouraged to register & process every recording with the Automation GUI just after recording has ended.

# Default use case

  1. Open the GUI just after recording has ended.
  2. Select the recording directory from dropdown list in section 1.
  • If no behavior associated with this recording uncheck ****
  1. Check "Add surgery & insertion device if missing" checkbox if you want to add electrode/microscope/optic fiber insertion coordinates.
  2. Select behavior session corresponding to recording from dropdown list in section 2.
  3. Click Register Recording button.
Automation GUI main screen
  • If no surgery data is found for the subject, a small form to insert surgery and device insertion coordinates will be shown.
Add surgery data form
  • Common coordinates for previous recordings:
Area ml(mm) ap(mm) depth(mm) theta(°) phi(°) rho(°)
mPFC L HEMIS -0.6 1.8 3.8 -45 -9 180
mPFC R HEMIS 0.6 1.8 3.8 45 9 0
HPC L HEMIS -1.5 2 1.8 -45 -9 180
HPC R HEMIS 1.5 2 1.8 45 9 0
  • Wait until recording has been copied to PNI storage resources (cup).
Dialog shown while copying session
  1. After recording has been transferred a small dialog with recording id will be shown.
Dialog shown when recording has been transferred
  1. User can check basic info of the new recording in the "Recording Table" tab. This tab will be active after recording is transferred.
Recording table tab screenshot

# Notes

  • This use case assumes that default parameters will be used to process the recording.

# "Advanced" (select parameters) use case

  1. Follow 1-4 from Default use case
  2. Uncheck "Use default processing parameters for recording?" checkbox
  3. Click "Select parameters >>>" button
Parameter selection main screen
  1. On the "Select parameters" tab (assume that all probes/fovs are going to be processed with same parameters)

# On section 1:

  1. In Preprocessing Params Lists dropdown Select a Preprocessing Param list
  • You can check which preprocessing steps are defined for that list on the listbox to the right)
  • If you select a preprocessing step from the listbox you can check the specific parameters for that preprocessing step on the text area to the right.

# On section 2:

  1. In Processing Params" dropdown select a Processing parameter suited for recording
  • If you select a processing parameter from the dropdown you can check the specific parameters for it on the text area to the right.
  1. Click Register Recording button.
  • Next actions are idential to the "Default use" case

# Monitor jobs

  • After a recording is submitted to processing the user is able to track, reprocess and visualize all jobs corresponsing to that recording.
Manage Processing Jobs main screen

# Track status

  1. Switch to "Manage Processing Jobs" tab.
  2. Use "User", "Subject" & "Date" dropdwons / edits to find desired jobs
  3. Select row corresponding to the corresponding job:
  • Corresponding Job Status history is shown for selected job.

# If status of job is in error status (-1, -2; "Error in recording process"):

  • You can open the Error log file on the bottom right corner by clicking "Open Error Log File" button.
  • If you consider that what cause the error is solved now, you can rerun job by clicking "Rerun job" button.

# If status of job is in finished status (7, 8; "Dat in element"):

  • You can open the Output log file on the bottom right corner by clicking "Open Output Log File" button.
  • You can visualize results from processing by clicking the bottom rightmost buttons: (Open Phy, Open IBL Atlas for ephys Open Suite2p-GUI for imaging)
Visualization tools available

# Rerun jobs

# Create new sets of processing parameters for recordings

  • In order to process recordings with parameters different than default you need at least one of the following:
  1. A new ser or processing parameters (parameters for the algorithm to process, e.g. kilosort, suite2p).
  2. A list of preprocessing steps formed by a set of preprocessing params (e.g. perform catgt + tprime before kilosort).
Create parameters screen

# Create new Processing parameters (algorithm pararms)

  • Note: You need a json file with all parameters ready before starting this process.
  • Here is an example of a kilosort parameter json file. It can serve you as an example for creating your own:
  1. Switch to "Create Parameters" tab.

# On section 0:

  1. In "recordig modality" dropdown select to which modality the parameters correspond.
  2. In "user" dropdown Select your NETID username (select general-user if this parameter will be shared by many users).

# On section 1a:

  1. In "proc. Param Method" dropdown, select which method (algorithm) these parameters refer to.
# If the algorithm is not found on "proc. Param Method" dropdown:
  • Check "define new proc. param method ?" checkbox.
  • Write new processing method name in "New Proc. Param. method" edit
  • Check automation pipeline developer guide to add corresponding processing code. (LINK MISSING)
  1. In "proc. Param Set Description" edit, write a small description for the new parameters.
  2. Click "Upload Proc-Parm Set json file" button and search/load for your json file with parameters. You can check your parameters on the text area on the right.
  3. Click "Register Proc. Param Set" button.

# Create new preprocessing parameters (a single step on preprocessing list)

  • Note: You need a json file with all parameters ready before starting this process.
  • Here is an example of a catgt parameter json file. It can serve you as an example for creating your own:
  1. Switch to "Create Parameters" tab.

# On section 0:

  1. In "recordig modality" dropdown select to which modality the parameters correspond.
  2. In "user" dropdown Select your NETID username (select general-user if this parameter will be shared by many users).

# On section 1b:

  1. In "Preproc.-Param Method" dropdown, select which method (tool) these parameters refer to.

# If the tool is not found on "Preproc.-Param Method" dropdown:

  • Check "define new prerproc.-param method ?" checkbox.
  • Write new preprocessing method name in "New Preproc.-Param method" edit.
  • Check automation pipeline developer guide to add corresponding preprocessing code. (LINK MISSING).
  1. In "Preproc.-Param Set Description" edit, write a small description for the new parameters.
  2. Click "Upload Preproc.-Parm Set json file" button and search/load for your json file with parameters. You can check your parameters on the text area on the right.
  3. Click "Register PreProc. Param Set" button.

# Create new preprocessing parameters list (a set of preprocessing paramaters)

  • Note: If you just created a preprocessing parameter, restart GUI.
  1. Switch to "Create Parameters" tab.

# On section 0:

  1. In "recordig modality" dropdown select to which modality the parameters correspond.
  2. In "user" dropdown Select your NETID username (select general-user if this parameter will be shared by many users).

# On section 1c:

  1. In "Pre-Params List Name" dropdown, write a suitable name for the list.
  2. In "Pre.-Param List Description" edit, write a small description for the new list.
  3. From "Pre.-Params steps" dropdown select the desired preprocessing step as part of the list.
  4. Click "Add Preparam Steps" button
  5. Repeat steps 6 & 7 to add all desired preprocessing steps for the list.
  6. Use "v" & "^" buttons to set order of preprocessing steps.
  7. Use "x" button to delete an unwanted preprocessing step.
  8. Click "Register pre param list" button.

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