Automation and interoperability
Tutorial
In this tutorial, we will explore two methods for downloading data: First, we will use the WEBKNOSSOS UI to download data as a Tiff stack. Then, we will learn how to automate this process using Python. Additionally, I will guide you through the process of incorporating an N5 remote dataset into WEBKNOSSOS. Let’s have a look!
WEBKNOSSOS makes it easy to download and export annotations as Tiff images. Start by creating a bounding box with the bounding box tool. Adjust it so that it covers the desired area.
Then, access the “Download” option from the dropdown menu and select “Tiff Export”. Choose which layer you want to export, and the bounding box covering the region you want to download. Click “export”, and that’s it! The Tiff stack will be saved in your download folder.
To automate this process with Python, follow the same initial steps. Select “Python client” in the download modal, then copy the provided code. You can also use the Python library documentation for more code examples to interact with your data.
Run the code on your computer to complete the process.
WEBKNOSSOS integrates seamlessly with other analysis softwares, enabling you to work with datasets from tools like Neuroglancer and Fiji. Let’s see an example of importing a Neuroglancer dataset to WEBKNOSSOS.
First, find the released dataset you would like to import online and copy its URL. In WEBKNOSSOS, click on “Add dataset” and select “Add remote dataset”. Paste the link, then click “Add layer”. Similar to adding local data, choose a target folder. Define a name for your dataset, set the voxel size, and click “import”. Once the dataset is imported, open it and enjoy the view!
That’s it, now you know how to export data using the UI or Python as well as how to work with remote datasets. Try out what you have learned now on webknossos.org! For more tutorials and updates on new features, follow us on Twitter or Mastodon.
