Examples¶

Nomenclature for CINPLA¶

Axona

FILENAME: “axona navn” e.g. 22031701, DATE: 220317, SESSION: 01, SUBJECT: subject-id e.g. 1704, ACTION-ID is thus SUBJECT-DATE-SESSION.

Open Ephys

FOLDERNAME: e.g. 1704_2017-05-13_13-52-26_03, DATE: 2017-05-13_13-52-26, which is automatically shortened to 130517, SESSION: 03, SUBJECT: subject-id e.g. 1704, ACTION-ID er thus SUBJECT-DATE-SESSION

NWB file structure and exdir

An action is stored in a folder named after the ACTION-ID. In this folder you will find main.exdir containing acquisition, general, analysis, processing. The acquisition contains all the raw data from your measuring instrument, processing contains extracted data which is and shall be processed. Finnaly, in the analysis folder, you will find figures etc. after analysis is perfomed.

General¶

Note that you can get all available commands with:

$ expipe --help

Furthermore if you want help on one particular command:

$ expipe transfer --help

Transfer data to and from server¶

Currently we support two means of transferring data: SCP (SSH), and copy. To maximize transfer speed we recomend using SCP (expecially on Windows). The SCP protocoll in expipe-plugin-cinpla is governed by the command transfer. In the config.yaml file (see installation page) you will find:

data_path: c:/users/uiousername/expipe_temp_storage
norstore:
  data_path: /norstore_osl/projects/NS9048K/server
  username: <norstore username>
  hostname: login.norstore.uio.no

Here norstore is the server name, the first data_path is the local path and the data_path under norstore we refer to as the server path. To transfer local data to the server, in it’s most simple form the transfer command can be used as:

$ expipe transfer ACTION-ID --from-local

This is because norstore is the default server name. In order to transfer to a different server we need to add it’s name with the --server command:

$ expipe transfer ACTION-ID --from-local --server processing

When you want to retrieve your data for manual analysis, you don’t want to download all the acquisition data, e.g. only processing and analysis. This can be achieved with the --exclude and --include:

$ expipe transfer ACTION-ID --to-local --include processing --include analysis

Note that many commands have a short name, e.g. --include can also be used with -i:

$ expipe transfer ACTION-ID --to-local -i processing -i analysis

Conversly if you want to transfer the entire action only excluding the acquisition:

$ expipe transfer ACTIO-ID --to-local --exclude acquisition

Registering subject¶

Subjects are registered under the project-id subjects-registry. This is to have a complete overview of animals in the lab i.e. active, dead, newborn which information is stored in tags. To register a subject use register-subject:

$ expipe register-subject SUBJECT --birthday 01.02.2017 --cell_line wild-type

Registering surgery¶

When performing surgery you can register information with the register-surgery command.:

$ expipe register-surgery SUBJECT --date 14.05.2017:12:35 --procedure implantation --weight 400

Drive adjustment¶

The first time you want to adjust the brain-area X, Y (reffering to PAR.TEMPLATES['implantation']['X']) of a drive an amount of um you need to initialize an adjustment action with the command:

$ expipe adjust SUBJECT --init

When you have initialized and later make a new adjustment:

$ expipe adjust SUBJECT --date dd.mm.yyyyTHH:MM --adjustment X um --adjustment Y um

Note that in stead of --date dd.mm.yyyyTHH:MM can use -d now.

Working with Axona¶

Open Anaconda 3 prompt:

activate phy

To get an overview of available commands::: expipe –help
For help på en spesifikk kommando::: expipe axona register –help

To overwrite existing data use --overwrite:

expipe axona register z:\USER\DATA\SUBJECT\FILENAME.set

Now modules are loaded to the firebase server and depth registration is promted to the user.

Spikesorting:

$ expipe spikesort ACTION-ID

Manual spikesoring with phy:

$ phy neo-gui c:\user\uiousername\expipe_temp_storage\ACTION-ID\main.exdir --channel-group 0

Save with ctrl-s

Working with Open Ephys¶

Open Anaconda 3 prompt:

activate phy

To get an overview of available commands::: expipe –help
For help på en spesifikk kommando::: expipe openephys register –help

To overwrite existing data use --overwrite:

expipe openephys register c:\open_ephys\data\1704_2017-05-13_13-52-26_03

Now modules are loaded to the firebase server and depth registration is promted to the user.

Todo

probefile etc.

Data processing:

$ expipe openephys process ACTION-ID

Todo

Detail the processing: ground channels, cmr vs car, filtering, probe

Manual spikesoring with phy:

$ phy neo-gui c:\user\uiousername\expipe_temp_storage\ACTION-ID\main.exdir --channel-group 0

Save with ctrl-s

Plotting og analysis¶

Plotting with notebook:

$ expipe generate-notebook ACTION-ID --run

kernel -> restart and run all

Make png figurer:

$ expipe analyse ACTION-ID --spatial

If you only want to look at a particular channel group:

$ expipe analyse ACTION-ID --channel-group 0

Register cells and transfer data to norstore

When your are finished with the analysis you want to produce a representation of the channel groups on the firebase server. This can be performed with the command:

$ expipe register-units ACTION-ID --tag GC --tag BC --message "found a beatiful grid cell on channel group 2"

Example tags: Bare dritt: no, Good shit: yes, Vet ikke: maybe, Head direction: HD, Grid cell: GC, Place cell: PC, Spatial cell: SC, Boarder cell: BC.

Go to SERVER/PROJECT/ACTION-ID/main.exdir/analysis to check out the results.