Updating pip package and compatibility with ZeroCostDL4Mic/DL4MicEverywhere

[esgomezm]

Hi there!

I'm updating the Embedseg notebook in ZeroCostDL4Mic so we can also use it in DL4MicEverywhere with Docker containers. For the containerisation in Mac we are having some issues that could be solved with some feature changes directly in EmbedSeg. We were wondering if the followings are easy or doable for you to deploy:

In the setup.py of embedseg, imagecodecs is listed as a dependency. Do you think it is be possible to remove it from the basic installation and leave it as an extra requirement for the environment?

Also, could it be possible to update the pip package with the new version of Embedseg? When installing it from pip there are multiple issues with old versions of numpy, however, when installing it directly from your repo, things work nicely.

Thank you! Sincerely,

Esti