Z-projections in Napari

Any chance that Napari will support Z-projections from within the graphic interface in the future? It would be nice to be able to select slices to make z-projections in the GUI and look at a Z-projection in the same instance of Napari in a separate layer.

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There’s a bit of work in this direction going on right now here:

In terms of whether it’s planned to do so e.g. even in 2D view: yes, right from the get-go. It’s our issue number 7! :joy:

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Hey @morpho ,

in the meantime, feel free to try napari-pyclesperanto-assistant. I liked your use-case and thus, just activated some transforms and projections in this napari plugin which do what you’re looking for. Install it using

conda install -c conda-forge pyopencl
pip install napari[all]
pip install napari-pyclesperanto-assistant==0.7.5

Start napari from command line:

napari

via napari’s menu, you can start the assistant:
image

Select a layer and click on transform:
image

Select the operation “sub stack” and enter the first and the last plane you want to project:
image

Afterwards, click on “Projection”:
image

And select the maximum projection.

If you color all three layers in different colours and switch to 3D and tiled view, you can see the effect of the operations.

You can then also select the second layer again and change the substack parameters and see the effect instantly:

pyclesperanto and its napari-assistant are experimental yet, and feedback is very welcome!

Cheers,
Robert

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Thank you! These are definitely features used often when looking through imaging data

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Thank you, I will give it a try soon and let you know how it goes!

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