How to record an animal experiment

How to record an animal experiment#

Requirements:

  • animal is already in DB, if not

  • you are added as user to DB, if not

Case 0: You stay stubborn and do things your way.#

Be my guest. But, be aware this is very likely to bite you in the *** at some point later. Also, you are on your own for animal sheets.

Case 1: You dont want to read datastructure, but just want to add an entry to the animal sheet.#

Metadata about where your data is stored is then not recorded to DB.

Options:

  1. Use WeightCommander and enter a behavior entry

  2. Enter using the Behavior-experiment template in eLabFTW. While one can add a file path to the meta field, its not ensured this path actually exists, or is transfered to DB.

  3. Use hardcore python to entry to DB.AnimalSheetEntry TODO reference jupyter tutorials

Case 2: you read the datastructure tutorial and recognized you will thank yourself later for using it#

Good on you.

Use SessionCommander to create and organize your sessions#

SessionCommander will give your session an easily identifiable session_id. As discussed previously its has the format %Y%m%d_animalid_%H%M%S. SessionCommander will also create the correct folder-tree inside your project folder. This will help you organize and find your files. Session commander also pushes the weight and information about the training/experiments to the labbook. Furthermore, metadata of your session will be recorded to the DataJoint DB, making it easy searchable and integratable into processing pipelines.

Use FileCommander to organize and copy your files to the correct place on the data server.#

You record different data modalities on different computers ? No problem, FileCommander can be used in a distributed manner. Install datastructure_tools on each computer and just select the correct session and copy the individual files for each modality.

Case 3: you would like to automate the folder creation, file copy and documentation#

We have built the tools with reuse in mind. The core functionality of SessionCommander etc. is available as separate modules. Those can be integrated in your custom software, etc. This will allow you to automate the procession of the session information, ensure adherence to the structure, reduce your manual work and human error. The Session class can be import from DB.utils and used to create sessions in DB, folders on the server etc. Please ask Florian or Artur for details and help in implementing this in your routine.

How-to delete/modify Sessions#

This usually should not be necessarily and is straight up a bad practice. Also, poorly executed experiments should be documented as such. Rather add some notes to the eLabFTW entry or DB. When using SessionCommander there will be no need to rename folder names or location.

We will occasionally run checks on the entries in DB and compare those with the dataserver. If folders remain empty for some time the session will be deleted. (Timelines and execution not decided yet).

You can remove the undesired session from the DB. This will only delete the metadata from DB. The entries to eLabFTW, if any as well as the files on the dataserver will remain untouched.

(DB.Session & {'session_id':'session to be deleted'}).delete()

I created a session for the wrong animal#

No worries, the session_id can be modified, as well as the corresponding filestructure on the data server.

TODO link or describe the util function to rename a session to a different animal.

written by: Artur
last modified: 2024-02-05