Accessing DCOR data

The deformability cytometry open repository (DCOR) allows you to upload and access RT-DC datasets online (internet connection required). The advantage is that you can access parts of the dataset (e.g. just two features) without downloading the entire data file (which includes image, contour, and traces information).

Public data

When you would previously download an entire dataset and do

import dclab
ds = dclab.new_dataset("/path/to/Downloads/calibration_beads.rtdc")

you can now skip the download and use the identifier (id) of a DCOR resource like so:

import dclab
ds = dclab.new_dataset("fb719fb2-bd9f-817a-7d70-f4002af916f0")

To determine the DCOR resource id, go to https://dcor.mpl.mpg.de, find the resource you are interested in, scroll down to the bottom, and copy the value from the id (not package id or revision id) field in (Additional Information). The DCOR format is documented in DCOR (online) format.

Private data

If you want to access private data, you need to pass a personal API Token:

import dclab
ds = dclab.new_dataset("fb719fb2-bd9f-817a-7d70-f4002af916f0",
                       api_key="XXXX-YYYY-ZZZZ")

You can manage your API Tokens on your profile page when logged in at https://dcor.mpl.mpg.de.

Alternatively, you can also set an API Token globally using

import dclab
from dclab.rtdc_dataset.fmt_dcor import APIHandler
APIHandler.add_api_key("XXXX-YYYY-ZZZZ")
ds = dclab.new_dataset("fb719fb2-bd9f-817a-7d70-f4002af916f0")

Managing API Tokens

You can manage your API Tokens on your profile page when logged in at https://dcor.mpl.mpg.de.

_images/DCOR_API_Token_website.png — Fig. 5 Managing API Tokens on DCOR.

Deleting a token:

Click on the tab “API Tokens” to view all currently existing tokens and the date they were last accessed. By clicking on the red “X” you can delete a token. It cannot be restored, so be careful when deleting tokens!
Creating a new token:

To create a new token, insert a name in the field at the top and click “Create API Token”. The newly generated token will be shown at the top of the page. Make sure you copy it directly, because you will not be able to recall it again!

Accessing data on a different DCOR instance

To access data on a different DCOR instance, you have to pass the respective URL when opening the dataset via the keyword host. The procedure to retrieve the DCOR resource id is the same as for the default DCOR.

import dclab
ds = dclab.new_dataset("fb719fb2-bd9f-817a-7d70-f4002af916f0",
                       host="dcor-dev.mpl.mpg.de")