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haesleinhuepf / bia-bob

BIA Bob is a Jupyter+LLM-based assistant for interacting with image data and for working on Bio-image Analysis tasks.
BSD 3-Clause "New" or "Revised" License
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add napari to the environment.yml #70

Open tischi opened 1 year ago

tischi commented 1 year ago

Is there a reason not to have napari in the list?

tischi commented 1 year ago

I think if napari is available it should default to using this as a viewer; we would need to adapt the prompt accordingly.

haesleinhuepf commented 1 year ago

Is there a reason not to have napari in the list?

I love using bia-bob in Jupyter-only environments such as on the HPC cluster / Jupyter hub / Google Colab. Napari doesn't work there.

Also Napari is slow and does not deliver insights such as intensity range, datatype etc., compared to stackview.insight that works instantaneously and brings these features.

image

I think if napari is available it should default to using this as a viewer; we would need to adapt the prompt accordingly.

I partially agree. This means we should dive into adapting the system message depending on installed libraries. A fair bit of work, but doable certainly.

haesleinhuepf commented 1 year ago

Addendum, this prompt already works fine with bia-bob 0.4.0:

%bob load c:/structure/data/blobs.tif and use napari to show the image

image

tischi commented 1 year ago

OK...

How many dimensions can stackview handle?

I think it errored for me with a 3D+channel image...

I do agree that having a nice and simple inline viewer would be awesome, but I am also afraid that we/you would at some point rewrite napari :-)

Also I think stackview should have a z-slider, should it? I could not get it to work....

haesleinhuepf commented 1 year ago

Also I think stackview should have a z-slider, should it? I could not get it to work....

Feel free to create issues on stackview's repository. Stackview does have a Z-slider and is supposed to work for 2D/3D-data. I recently added support for RGB-data. 4D-data is rare in my daily work as we typically setup workflows for individual timepoints and later run it on an entire timelapse dataset. But I happy to learn more about your use case. And adding another slider is not a big deal I guess.