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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.
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.
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.
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tischi commentedon Nov 2, 2023
Is there a reason not to have napari in the list?
tischi commentedon Nov 2, 2023
I think if napari is available it should default to using this as a viewer; we would need to adapt the prompt accordingly.
haesleinhuepf commentedon Nov 2, 2023
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.insightthat works instantaneously and brings these features.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 commentedon Nov 2, 2023
Addendum, this prompt already works fine with bia-bob 0.4.0:
tischi commentedon Nov 2, 2023
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 commentedon Nov 2, 2023
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.