pathml VS Dask

We have been using dask to support our computational pathology workflows [1], where the images are so big that they cannot be loaded in memory, let alone analyzed (standard pathology whole slide images are ~1GB; some microscopy techniques generate images >1TB). We divide each image into a bunch of smaller tiles and process each tile independently. The dask.distributed scheduler lets us scale up by distributing the tile processing across a cluster.

Benefits of dask.distributed: easy to get up and running, and has support for spinning up clusters on lots of different computing platforms (local machines, HPC cluster, k8s, etc.)

One difficulty is optimizing performance - there are so many configuration details (job size, number of workers, worker resources, etc. etc.) that it's been hard to know what is best.

[1] https://github.com/Dana-Farber-AIOS/pathml

Data scientists work on phenomenally large datasets, and Dask is a handy tool for exploration within the confines of a single cloud VM or their local PCs. Location data visualization is an essential part of deciding further algorithm development and roadmap for projects. This lays the foundation for data engineering and science to work at scale, with petabytes of data.

Dask

We're using a lot of Python. In addition to these, gridMET, Dask, HoloViz, and kerchunk.

I wrote this for speeding up the RPC messaging in dask, but figured it might be useful for others as well. The source is available on github here: https://github.com/jcrist/msgspec.

Dask: Distributed data frames, machine learning and more

To do that, we are efficiently using Dask, simply creating on-demand local (or remote) clusters on task run() method:

Look into Dask, see: https://dask.org/

[1] https://dask.org/