Version 1: changes to the cellfinder backend and plugin

The cellfinder-core package and cellfinder-napari plugin have now been migrated to a package called cellfinder. Please note that this is enacting the future warning from the earlier cellfinder (CLI) migration. If you wish to continue using both the cellfinder command-line interface and the backend Python API, you will need to install the latest version of brainglobe-workflows, which will automatically fetch the new version of the cellfinder package. See the updating section for more details.

cellfinder-core

If you were previously using the Python API to cellfinder-core, you will need to uninstall cellfinder-core from your environment and install cellfinder version 1.0.0 or later.

The internal package structure has not changed in this move, but it is now a submodule of the new cellfinder package. So if you were using the Python API in your scripts, you will need to change any from cellfinder_core import X statements to from cellfinder.core import X. Once you make this change, everything should work as it was before.

cellfinder-napari

If you were previously using the napari plugin for visualising output data, you will need to uninstall cellfinder-napari and install cellfinder[napari], making sure to fetch the optional napari dependency.

The plugin itself has not undergone any interface changes, but is now just called “cellfinder” rather than “cellfinder-napari” when viewed from the napari widget panel.

brainglobe-workflows

Now ships with the new version of cellfinder, containing cellfinder.core and cellfinder.napari submodules. brainglobe-workflows is now the only package that provides the old “cellfinder” command-line interface, or workflow. This workflow is now only available under the name brainmapper - the name cellfinder is reserved for the backend package that contains the merged cellfinder-core and cellfinder-napari packages mentioned above.

Updating

The update steps that you will need to perform vary depending on how you currently use cellfinder (CLI) and whether you upgraded to brainglobe-workflows previously. Regardless, before you begin the process of updating we recommend you uninstall cellfinder-core and cellfinder-napari from your environment

pip uninstall cellfinder-core cellfinder-napari

Alternatively; you can create a new, clean environment to install into.

I previously updated to brainglobe-workflows

If you previously updated from the old cellfinder package to brainglobe-workflows, then you should be able to simply update to the latest version of brainglobe-workflows, with

pip install --upgrade brainglobe-workflows

This will fetch the new cellfinder package containing the cellfinder.core and cellfinder.napari submodules. You can then continue to use the CLI to run the workflow as you were doing before, however note that the workflow will now only be available as “brainmapper”.

I have not updated to brainglobe-workflows, but I don’t use the cellfinder CLI

If you don’t use the cellfinder CLI, then you can just upgrade your version of the cellfinder package to version 1.0.0 or later:

pip install --upgrade cellfinder

If you do want to make use of the old “cellfinder” workflow, you will need to install brainglobe-workflows and use it under its new name, brainmapper.

I have not updated to brainglobe-workflows, and I use the cellfinder CLI

In this case, we strongly recommend you either create a new Python environment to install into (and delete your old one), or remove cellfinder, cellfinder-core, and cellfinder-napari from your current environment with

pip uninstall cellfinder cellfinder-core cellfinder-napari

You may also wish to use pip to uninstall tensorflow to make sure that the new install does not encounter potential version conflicts.

Once you have cleaned your environment, you will need to install the latest version of brainglobe-workflows:

pip install brainglobe-workflows

You will now have access to the brainmapper workflow from within your environment. This is the same as the old “cellfinder” workflow that you were using previously - but now it is supplied by the brainglobe-workflows package. You will also have the latest version of the cellfinder package (1.0.0 or later) installed;

• cellfinder-core is included as a submodule, cellfinder.core.

• cellfinder-napari is included as a submodule, and the plugin has been renamed to just “cellfinder” when viewed in napari.

• To access the old “cellfinder” command-line tool or workflow, you now need to call brainmapper. The interface has not changed, just the name.