Process Drosophila_3D+t stack in parallel using Azure Batch Python API

[wolny]

Resubmitting the PR made under lmiroslaw/azure-batch-ilastik#3 as suggested by @lmiroslaw lmiroslaw/azure-batch-ilastik#3 (comment)

This PR shows how to processes the 5D tensor containing the stack of Drosophila embryo in parallel using ilasitk running on Azure Batch via Python API. The app uploads the stack into a single storage container and then segments the nuclei via a parallel workload running 50 ilastik processes (there are 50 time points in the stack, it's one segmentation task per time point) in a headless mode (see http://ilastik.org/documentation/basics/headless from more information). The output of each segmentation task (one tiff file per time point containing segmented 3D stack) is uploaded to a single storage container and then downloaded into the current working dir.

Prerequisites

• python 3.6
• pip3

Run the app

• Install virtualenv pip3 install virtualenv
• Go into the python dir and create virtual env for the app cd python && python3 -m virtualenv env
• Install required packages: pip install -r requirements.txt
• Update the Batch and storage account credentials inside the ilasik_azure_batch_client.py
• Run the script: python ilasik_azure_batch_client.py
• Wait for the script to finish and check that the output segmentation files have been successfully downloaded into your current directory (the files should be named drosophila_00-49_{t}_seg.tiff, where t corresponds to a given time point in the stack).

Sample segmentation output

Output of the ilastik segmentation task for a sample time point: