Version 1: Cellfinder migration and brainglobe-workflows#


Due to some historical naming decisions, there are some unfortunate clashes of language between packages, workflows, and tools. We disambiguate these terms before proceeding with the changelog:

  • “workflow” refers to an analysis pipeline - a sequence of data analysis steps to process data and produce an output, using a combination of BrainGlobe tools.

  • brainglobe-workflows refers to the new package released with this update. Source code on GitHub.

  • cellfinder (package) refers to the package named cellfinder on PyPI. Specifically, to any versions <1.0.0 of this package.

  • cellfinder (repository) refers to the source code on GitHub.

  • cellfinder (CLI) refers to the cellfinder command-line tool. This is provided by both cellfinder (package) and brainglobe-workflows.

  • cellfinder (Docker image) refers to the Docker image that allows users to mount their data and run cellfinder (CLI).

Python version support#

With this update, we are dropping cellfinder (CLI) support for Python 3.8. Whilst the workflow should still run on Python 3.8 in the immediate future, the oldest supported version is now Python 3.9.

cellfinder (package)#

This package should now be considered deprecated to users. Consequently, the cellfinder (CLI) tool provided by this package will no longer receive updates. If you want to keep the cellfinder (CLI) up to date, you will need to install brainglobe-workflows and use the cellfinder (CLI) provided there.


For development purposes, cellfinder (package) will later become the new name for the combined cellfinder-core and cellfinder-napari package. This release of the package will be tagged with version >=1.0.0, to indicate that a breaking change has occurred, and there will be a corresponding blog post published.

If you have not moved to using cellfinder (CLI) provided by brainglobe-workflows, this change will break your analysis pipelines if you try to update. You will need to install either brainglobe-workflows or BrainGlobe version 1, or prevent your package manager from attempting to update cellfinder (package).

cellfinder (repository)#

For development purposes, the cellfinder repository will be recycled to include the backend code that is currently stored in cellfinder-core and cellfinder-napari. Similarly to brainreg, we will be combining the functionality of the backend code and visualisation tool into a single package.

cellfinder (Docker image)#

We will no longer be providing Docker images for cellfinder (CLI). We recommend that you install brainglobe-workflows, or BrainGlobe version 1 when it is release, into a clean virtual environment as an alternative.


This package now provides the cellfinder (CLI) tool, and is the recommended way to run the analysis pipeline. It can be installed via pip - see the instructions below.

This package will continue to grow to include additional analysis pipelines and workflows for data analysis in neuroscience.

Updating to the new cellfinder (CLI) tool#

In order to update to the new cellfinder (CLI) tool provided by brainglobe-workflows, follow the steps below:

  1. Uninstall cellfinder (package) from your Python environment. This should be a case of running pip uninstall cellfinder on the command line, with the environment activated.

  2. (Optional) verify that the cellfinder (CLI) tool has been removed. If the output of which cellfinder is nothing, then the old tool has been successfully removed.

  3. Install brainglobe-workflows into your environment. Again, we recommend installing via pip: pip install brainglobe-workflows.

  4. (Optional) verify that the (new) cellfinder (CLI) tool has been installed. The output of which cellfinder should display a path to your activated environment, which ends inside the brainglobe-workflows package.

If you are making a clean install into a fresh environment, there is no need to run the first two (uninstall) steps. Simply pip install brainglobe-workflows into your new environment.

As mentioned in the main blog post, cellfinder (CLI) will also be getting a new name in the near future, as additional workflow tools are added. It’s name isn’t changing right now, but keep an eye on this space.

Delaying updating#

We strongly recommend you move to using brainglobe-workflows if you wish to continue using the cellfinder (CLI) tool.

If you really want to keep using the old cellfinder (package), you will need to prevent further updates to it. The cellfinder (CLI) provided by cellfinder (package) will continue to work so long as you do not update, however you should consider any versions of cellfinder (CLI) provided by cellfinder (package) unmaintained. You will eventually run into the name conflicts listed above, as BrainGlobe version 1 starts to roll out.