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Update ImageJ2/Fiji version in the docs and improve toc layout #276

Merged
merged 13 commits into from
Aug 10, 2023
Merged

Update ImageJ2/Fiji version in the docs and improve toc layout #276

merged 13 commits into from
Aug 10, 2023

Commits on Aug 8, 2023

  1. Change code block language hint to bash 

    Sphinx doesn't like "!pip" with a python language
code block.
    @elevans
    elevans committed Aug 8, 2023
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  2. Update imagej version from 2.5.0 to 2.13.1

    @elevans
    elevans committed Aug 8, 2023
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  3. Bump minimum version recommendation to 2.11.0

    @elevans
    elevans committed Aug 8, 2023
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  4. Remove references to the dummy ImagePlus HACK

    @elevans
    elevans committed Aug 8, 2023
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  5. Replace blood vessel image with hela in metaphase 

    The blood vessel image is no longer available. This commit
swaps the blood vessel image with a slice from a 4D dataset that
contains microtubules in metaphase.
    @elevans
    elevans committed Aug 8, 2023
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  6. Re-run notebooks with ImageJ2 2.13.1 

    Re-run all jupyter notebooks and save their output with
ImageJ2 version 2.13.1.
    @elevans
    elevans committed Aug 8, 2023
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  7. Reorganize read the docs toc 

    This commit reorganizes the table of contents
for the read the docs site. I added sections and emojis to
enhance readability and create a more welcoming experince for
visitors.
    @elevans
    elevans committed Aug 8, 2023
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  8. Remove note about Fiji stderror warnings

    @elevans
    elevans committed Aug 8, 2023
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  9. Update ImageJ2/Fiji version to 2.14.0

    @elevans
    elevans committed Aug 8, 2023
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  10. Fix wrong NumPy conversion type 

    NumPy arrays go to `net.imagej.DefaultDataset` and don't
make an `ImgView`.
    @elevans
    elevans committed Aug 8, 2023
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  11. Remove itkwidgets error 

    I accidentally ran the notebook without itkwidgets
and pushed the output.
    @elevans
    elevans committed Aug 8, 2023
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  12. Fix cell detection dataframe output 

    The output was only displaying the first cell.
I also fixed the column names. Pandas thought
it was a multi-level column name.
    @elevans
    elevans committed Aug 8, 2023
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  13. Regenerate notebook content 

    We fixed a duplicating stdout and stderr in commit
d99fcf0 thus we need to recreate the notebook outputs.
    @elevans
    elevans committed Aug 8, 2023
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