Command Line Interface: Creating a collection

Once Zegami has been installed a collection of images can be made by using the Command Line Interface or CLI for short.

The CLI can be accessed by opening up the terminal or command prompt and running the following command:

Collection Creation

The collection we are going to create in this tutorial is of Xenopus embryo (a type of frog used in research) at different stages of life cycle (STAGE). These have had certain genes (TARGET GENE) that are shown to be expressed in the embryo which highlighted by the dark staining. CONCENTRATION is concentration of morpholino which is used to modify the gene expression.

The example source data and configuration files can be downloaded from here (~3 Mb). These images have kindly been donated from Roger Patient’s lab in Oxford (http://www.imm.ox.ac.uk/roger-patient). Download and extract these files to a location that can be accessed by Zegami. For Linux extract them to /zegami/data-source/xenopus. For Windows extract them to C:\zegami\data-source\xenopus.

Processing a Collection using Zegami CLI

Once the tutorial files have been downloaded and extracted the Xenopus collection can be processed. If the files were extracted to a location other than the recommended locations listed above then the locations in both the datasource.conf and imagesource.conf will need to be updated. If you have a problem processing a collection please ensure to include the contents of these files in any support request.

imagesource.conf

This file contains the details about the location of the images. It uses the imagesPath value to retrieve the images. The path is also dynamic, meaning that it is data bound to the corresponding row in the data source.

For example if the data source has a column called path which contains values like "image001.jpg", "image002.jpg" and "image003.jpg"... the value of the path column can be included in the path string by enclosing it in double ' and ', like so: ''.

The structure of the file is as follows, with comments.

datasource.conf

This file contains the details about the location and structure of the metadata. The structure of the file is as follows, with comments.

Processing

For Linix open a terminal and run the following command:

For Windows open the command prompt and navigate to C:\Program Files (x86)\Zegami and run the following command:

The collection will now be created and processing will commence. Once completed the collection details will be displayed:

For more details on using Zegami CLI see our detailed guide of all the commands.