Documentation for QC LIMS usage:

[seanmcculloch]

qc-sys-webapp uses the lims2 DB and queries the following tables and columns:

Tables and Columns

1. ophys_sessions (os):

   • id
   • name
   • workflow_state
   • storage_directory
   • specimen_id
   • date_of_acquisition
   • stimulus_name
   • operator_id
   • project_id
   • equipment_id
   • parent_session_id
   • isi_experiment_id
   • foraging_id

2. ophys_experiments (oe):

   • id
   • name
   • workflow_state
   • storage_directory
   • ophys_session_id
   • imaging_depth_id
   • targeted_structure_id
   • ophys_imaging_plane_group_id

3. isi_experiments (isi):

   • id
   • name
   • workflow_state
   • storage_directory

4. users (u):

   • id
   • login

5. projects (p):

   • id
   • code

6. equipment (e):

   • id
   • name

7. specimens (sp):

   • id
   • external_specimen_name
   • name

8. imaging_depths (imd/dp):

   • id
   • depth

9. structures (st):

   • id
   • acronym

10. behavior_sessions (bs):

    • id
    • foraging_id
    • date_of_acquisition
    • donor_id
    • equipment_id
    • user_id

11. donors (d):

    • id
    • external_donor_name

12. images (im):

    • id

13. scans (sc):

    • image_id

14. scanners:

    • id
    • name

15. ophys_experiments_visual_behavior_experiment_containers (subquery earliest_containers):

    • visual_behavior_experiment_container_id
    • ophys_experiment_id

Mindscope_qc_metrics Uses a combination of lims db queries and actual data files. Using an example of:

session_id = 1324966817
project = 'LearningmFISHTask1A'

The following datasets loaded these specific data files:

Directory: /allen/programs/mindscope/production/learning/prod0/specimen_1315419106/ophys_session_1324966817/

behavior_video 1324966817_Behavior_20240119T093807.mp4

behavior_video_meta *_Behavior_*.h5

eye_tracking_video 1324966817_Eye_20240119T093808.mp4

eye_tracking_video_meta *_Eye_*.h5

face_tracking_video 1324966817_Face_20240119T093808.mp4

face_tracking_video_meta 1324966817_Face_20240119T093808.json

motion_corr_physio ophys_experiment_1325101125/processed/1325101125_suite2p_motion_output.h5

motion_corr_physio_meta No filepath

local_z_stack ophys_experiment_1325101125/1325101125_z_stack_local.h5

local_z_stack_meta No filepath

rig_sync 1324966817_20240119T093757.h5