Getting started

Expipe can be used to manage multiple projects. Each project consists of collections of actions, entities, templates and project modules.


Create a new project with the require_project function:

import expipe
project = expipe.require_project("test")

The default backend for Expipe uses the filesystem. In this case, the above command will create a folder named test in your current working directory. Other backends will create a backend-specific project in its database.


Actions are events that are performed during a project. An action can be an experiment, preparations for an experiment, or an analysys performed after an experiment.

To create an action on the project or return an existing action if it already exists, use project.require_action:

action = project.require_action("something")

Action attributes

To give actions easily searchable properties you can add Tags, Users, Subjects and Datetime

from datetime import datetime
action.tags = ['place cell', 'familiar environment']
action.datetime =
action.location = 'here'
action.type = 'Recording'
action.subjects = ['rat1']
action.users = ['Peter', 'Mary']


Actions have multiple properties such as the type, location, users, tags and subjects. If you want to expand an action with more information, you can use modules. Modules can hold arbitrary information about the action and can be predefined by using templates to make it easy to add the same information to multiple actions. Ideally, templates should be designed in the beginning of a project to define what should be registered in each action.

To add a module to an action, use require_module. The function takes an optional template parameter:

tracking = action.require_module("tracking", template="tracking")

If you are not using templates you may also create modules using dictionaries:

import quantities as pq
tracking_contents = {'box_shape': {'value': 'square'}}
tracking_module = action.require_module(name="tracking",
elphys_contents = {'depth': 2 *, }
elphys_module = action.require_module(name="electrophysiology",

You can loop through modules in an action similarly to a dictionary:

for name, val in action.modules.items():
     if name == 'electrophysiology':
2.0 um

To further retrieve and edit the values of a module, you can use the module.to_dict():

tracking = action.require_module(name="tracking")
OrderedDict([('box_shape', {'value': 'square'})])

From Template to Module

To upload a template you can write it as a dict and use require_template.

daq_contents = {
    "channel_count": {"definition": "The number of input channels of the DAQ-device.",
                      "value": "64"}}

In order to use a template and add it as a module to an action use action.require_module:

daq = action.require_module(template='hardware_daq')

Now, the template hardware_daq is added to your action as a module and you also have it locally stored in the variable daq. To retrieve daq keys and values use to_dict:

daq_dict = daq.to_dict()
odict_values([{'definition': 'The number of input channels of the DAQ-device.', 'value': '64'}])


If you want to expand an action with notes and messages, you can use messages. Messages are annotations from users that are involved with an action. To add a message to an action you can run:

from datetime import datetime
messages = [{'message': 'hello', 'user': 'Peter', 'datetime':}]
action.messages = messages