If you are running a High Content Screening Pipeline you probably have a lot of moving pieces. As a non exhaustive list you need to:
These tasks are much easier to accomplish when you have a system or framework that is built for scientific workflows.
If you prefer to watch I have a video where I go through all the steps in this tutorial.
Apache Airflow is :
Airflow is a platform created by the community to programmatically author, schedule and...
For a few years now I have been on a quest to find a tool I really like for annotating HCS images using a web interface. I've used several tools, including a desktop application called LabelImg, and I have finally found a tool that checks all the boxes called LabelStudio!
Label Studio is an annotation tool for images, audio, and text. Here we'll be concentrating on images as our medium of choice.
I go through the process in this video.
You can, of course, use your own data, but for this tutorial I will be using a publically available C. elegans dataset from the Broad BioImage Benchmark Collection.
mkdir data cd data wget https://data.broadinstitute.org/bbbc/BBBC010/BBBC010_v2_images.zip unzip BBBC010_v2_images.zip
HCS images are often very dark when opened in a system viewer. To use them for the rest of the pipeline we will have to do a two step conversion process, first using bftools to convert from tif -> png, and then using Imagmagick to do a levels...
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