mesoSPIM-lazy-loader

Lazy-loader for mesoSPIM acquisitions using napari. This plugin simply lazy-loads all mesoSPIM TIFF stacks in a directory, color-coding channels according to the excitation laser. The goal is to provide a quick way of visualising non-tiled acquisitions. Once installed, you can open a folder containing a mesoSPIM acquisition and the plugin will lazy load it. For best results organise your acquisitions so each folder contains data from a single resolution and view (i.e. data from different orientations or locations should be in different directories).

Known issues

• Works only with TIFF stacks that have associated meta-data files
• Will load both shutters and overlay them. (TODO: add a widget to allow switching between shutters using a button)
• Since it lazy-loads each plane as required using dask, it will cause napari to freeze if the user requests a 3D view or a reslice view. Some solution is needed for this. e.g. disable the buttons.
• Color-coding assumes excitation lines named 647 nm, 561 nm, 488 nm, and 405 nm.

---

Installation

If you don't already have a suitable environment for napari, you can create one with:

conda create -y -n napari-env -c conda-forge python=3.9
conda activate napari-env

On Apple Silicon you likely must do it the above way or the install will fail.

This plugin is not yet on PyPi or napari hub so you should do either:

• pip install git+https://github.com/mesoSPIM/mesoSPIM-lazy-loader.git@main (If you get an error about git being a missing command, you likely just need to first conda install git)
• or download from GitHub, cd to the downloaded directory, and pip install .

Install failure on Apple Silicon

If the installation stalls on Apple Silicon at Preparing metadata (pyproject.toml) ... you can try ctrl-c to break out and append --config-settings --confirm-license= --verbose to your pip command. e.g.

pip install git+https://github.com/mesoSPIM/mesoSPIM-lazy-loader.git@main --config-settings --confirm-license= --verbose

The failure is because PyQt5 has asked for a response to a licence agreement and was watiting for a reply.

Instructions

Use the plugin to load a directory containing mesoSPIM tiff files.

Contributing

Contributions are very welcome. You can set up tests with tox (none yet), please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the GNU GPL v3.0 license, "mesoSPIM-lazy-loader" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.