Installation
From Napari interface
FishFeats is a Napari plugin, in python. You can install it either through an already installed Napari instance by going in Napari to Plugins>Install/Uninstall, search for FishFeats and click Install.
You could have version issues between the different modules installed in your environment and FishFeats dependencies, in this case it is recommended to create a new virtual environnement specific for FishFeats.
From virtual environnement
To install FishFeats, you should create a new virtual environnement or activate an exisiting compatible one.
Create a new virtual environement
You can create a virtual environement with venv or anaconda (you may need to install anaconda, see here: on windows, on macOS or on linux ).
Then use the Anaconda interface to create a new virtual environement with the desired python version, or through the Terminal.
For example, in a terminal, once conda is installed, you can create a new environnement by typing:
Install FishFeats
Once you have created/identified a virtual environnement, type in the terminal:
to activate it (and start working in that environnement).Type in the activated environnement window:
to install FishFeats.Installation of dependencies
As the plugin relies on several different python modules and for flexibilit, we don't enforce the install of all dependencies on the basic installation of FishFeats.
It is up to the user to install the extra dependencies that will be usefull for her/his project.
However, it is possible to install directly most of the main dependencies by installing fishfeats with the full option: pip install fishfeats[full]
Start FishFeats
Open Napari by typing
in the activated environnement and goes toPlugins>FishFeats>Start fishfeats
Compatibility/Dependencies
FishFeats depends on several python modules to allow different tasks. It is not necessary to install all the dependencies to run it, only the ones listed in setup.cfg configuration file. When installing the plugin, the listed dependencies will be automatically installed.
Other dependencies can be installed individually if the corresponding option will be used (e.g. install cellpose: pip install cellpose).
They can also be all installed by installing FishFeats in full mode pip install fishfeats[full].
Operating System
The plugin has been developped on a Linux environment and is used on Windows and MacOS distributions. It should thus be compatible with all these OS provided to have the adequate python environments.
Windows GPU card nvidia A6000
We encountered an unsolved yet error only on Windows with some specific nvidia drivers/GPU card. During plugin usage, it returns this error:OSError: exception: access violation reading 0x0000000000000034. See here for more infos.
Python version
We tested the plugin with python 3.9, 3.10, with Napari 0.4.19, 0.6.1.
In Trouble shooting, we listed some environnement that worked for given operating system/python version.
You can also create your environment directly from these .yaml files.
There is an incompability with Napari 0.4.17 (strongly not recommended) for point edition in 3D.
Please refers to Trouble shooting if you encounter issues at the installation/usage or to the repository issues. Finally if you don't find any information on your error, open a new issue in this repository.