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Update the ome_zarr channel #728

Merged
merged 568 commits into from
Sep 27, 2024
Merged

Update the ome_zarr channel #728

merged 568 commits into from
Sep 27, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Mar 19, 2024

  1. Merge branch 'master' into volume_slicing_anniek

    @AnniekStok
    AnniekStok authored Mar 19, 2024
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  2. Merge pull request #630 from NEUBIAS/volume_slicing_anniek 

    Volume slicing refactoring
    @tischi
    tischi authored Mar 19, 2024
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Commits on Mar 25, 2024

  1. Init using LLMs to generate code

    @tischi
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  2. Creating code using a LLM

    @tischi
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Commits on Mar 26, 2024

  1. Improve coding with LLMs

    @tischi
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  2. Improve coding with LLMs

    @tischi
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Commits on Mar 28, 2024

  1. Update 2024_scientific_image_inspection_and_presentation.md

    @tischi
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  2. Update TEACHING_TIPS.md

    @tischi
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  3. Update TEACHING_TIPS.md

    @tischi
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  4. Update TEACHING_TIPS.md

    @tischi
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  5. microscopy_data_inspection WIP

    @tischi
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  6. Merge branch 'master' of https://github.com/NEUBIAS/training-resources

    @tischi
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Commits on Mar 29, 2024

  1. Init Similarity Transforms module

    @tischi
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Commits on Mar 31, 2024

  1. Init script to automatically create figures, #636

    @tischi
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  2. Add create_modules_pdf.sh #636

    @tischi
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  3. Improve script to create a PDF presentation of selected modules, #637

    @tischi
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Commits on Apr 10, 2024

  1. add some galaxy instructions

    @sunyi000
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Commits on Apr 15, 2024

  1. add 2024_skimage_napari_beginners.md

    @tischi
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  2. Update 2024 python course

    @tischi
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Commits on Apr 18, 2024

  1. meadian filter

    @sunyi000
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  2. Merge branch 'master' into galaxy

    @sunyi000
    sunyi000 committed Apr 18, 2024
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  3. fix typo

    @sunyi000
    sunyi000 committed Apr 18, 2024
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Commits on Apr 21, 2024

  1. Move OpenIJTIFF functionality to own module 

    in preparation of creating a python package out of it.
    @k-dominik
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  2. Fix codestyle, docstrings, typing 

    * Ran black for a more objective code style
* Fixed some type annotations (mostly in order to understand the better
  understand the code
* Added more docstrings mostly in order to better understand the code
* Ensured google-style docstrings
    @k-dominik
    k-dominik committed Apr 21, 2024
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Commits on Apr 22, 2024

  1. Update 2024_skimage_napari_beginners.md

    @tischi
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Commits on Apr 23, 2024

  1. factor out downloading function 

    Note: This changes the behavior a bit. Previous version was opening the
tiff file and immediately unlinking the file, such that it was deleted
once tifffile closed the handle. However, this was not supported on
windows, where a blank try except was employed to hide it and also
obscure what was really happening. Now the behavior on all osses is the
same and users can employ the os-specific way to clean up their temp
folder.
    @k-dominik
    k-dominik committed Apr 23, 2024
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  2. add (ugly) typing to open_ij_tiff returns 

    would prefer to remove the special handling of fetching extra metadata
as it's also not used in the tutorial.
Typing gets ugly with the different return types.
    @k-dominik
    k-dominik committed Apr 23, 2024
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  3. Added minimal conda recipe + pyproject.toml

    @k-dominik
    k-dominik committed Apr 23, 2024
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  4. remove unecessary path manipulation 

    it's also not really good practice.
    @k-dominik
    k-dominik committed Apr 23, 2024
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Commits on Apr 24, 2024

  1. Merge pull request #647 from NEUBIAS/move-openij-python-to-module 

    Move OpenIJTIFF python to module/conda-package
    @tischi
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  2. Update 2024_skimage_napari_beginners.md

    @tischi
    tischi authored Apr 24, 2024
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Commits on Apr 25, 2024

  1. Updated installation instructions 

    * `openijtiff` now sourced from `euro-bioimaging` conda channel
* open `.py` files as notebooks via right-click in jypyter.
    @k-dominik
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  2. Merge pull request #648 from NEUBIAS/enh-install-instructions-conda 

    Updated installation instructions
    @bugraoezdemir
    bugraoezdemir authored Apr 25, 2024
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  3. Added tests for python scripts in _includes

    @k-dominik
    k-dominik committed Apr 25, 2024
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  4. ignore jython scripts

    @k-dominik
    k-dominik committed Apr 25, 2024
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  5. Modify 2024_skimage_napari_beginners.md

    @tischi
    tischi committed Apr 25, 2024
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  6. Merge latest main

    @tischi
    tischi committed Apr 25, 2024
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  7. Fix scripts to allow test running 

    * `binarization_skimage_napari.py`: use `OpenIJTIFF` to open image from
  the internet.
* `filter_morphological_ac1_skimage_napari.py`: use `add_image` in both
  instances after morphological operations. `add_labels` does not take
  a colormap
* `sptial_calibration_act2_skimage_napari.py`: write to home folder,
  added note for trainings - should be replaced by users Desktop folder.
* `string_concat_python.py`: remove semi-colons, fix typo.
    @k-dominik
    k-dominik committed Apr 25, 2024
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Commits on Apr 26, 2024

  1. Add xfail expectations for some tests 

    some tests require manual interactions of some kind or are run in a
different environment - e.g. not from a notebook but in napari directly.
Those xfail now with appropriate reasons.
    @k-dominik
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  2. Merge pull request #649 from NEUBIAS/add-tests-python 

    Added tests for python scripts in _includes
    @bugraoezdemir
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  3. Improve pixels_act1_skimage_napari.py

    @tischi
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  4. Merge branch 'master' of https://github.com/NEUBIAS/training-resources

    @tischi
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  5. Merge branch 'improve_digital_image_basics_python'

    @tischi
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  6. Fixes #646

    @tischi
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  7. Improve pixels_act1_skimage_napari.py, remove markdown #651, Fixes #629

    @tischi
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Commits on Apr 27, 2024

  1. Implement pixels_3d_image_inspection_skimage_napari.py

    @tischi
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  2. Improve the python LUT activities

    @tischi
    tischi committed Apr 27, 2024
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Commits on Apr 28, 2024

  1. fix missing square bracket

    @k-dominik
    k-dominik committed Apr 28, 2024
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  2. Merge pull request #655 from NEUBIAS/quickfix-py-pixels-act1 

    fix missing square bracket
    @tischi
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Commits on Apr 29, 2024

  1. Update schedule

    @tischi
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  2. datatypes: simplifying image loading calls

    @jhennies
    jhennies committed Apr 29, 2024
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  3. various updates

    @sunyi000
    sunyi000 committed Apr 29, 2024
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  4. updates and merge with the latest main

    @sunyi000
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  5. instruction to install galaxy tool

    @sunyi000
    sunyi000 committed Apr 29, 2024
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  6. Fixes #660; it turned out that this was actually quite OK already

    @tischi
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  7. Simpliy LUTs activity for skimage napari

    @tischi
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  8. Improve pixels_act1_skimage_napari.py

    @tischi
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  9. Improve binarization_act*_skimage_napari

    @tischi
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  10. Improve binarization_act2.md

    @tischi
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  11. added aspect ratio formula to 'measure_shapes_act1.md'

    akhan committed Apr 29, 2024
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Commits on Apr 30, 2024

  1. Start working on improving datatypes_act1_skimage_napari.py

    @tischi
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  2. fix missing import in binarization_act2_skimage_napari.py

    @tischi
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  3. Add missing imports to binarization_act2_skimage_napari.py

    @tischi
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Commits on May 3, 2024

  1. new MoBIE CLEM module

    @martinschorb
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  2. manual registration

    @martinschorb
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Commits on May 6, 2024

  1. Minor changes to filter_mean_skimage_napari.py

    @tischi
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  2. simplify filter_variance_skimage_napari.py, but introduce the concept… 

    … of a function
    @tischi
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  3. Improve median_filter_skimage_napari.py

    @tischi
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  4. Improve local_background_correction_act1_skimage_napari.py

    @tischi
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  5. Improve local_background_correction_act2_skimage_napari.py

    @tischi
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  6. Merge pull request #674 from NEUBIAS/improve_median_filter_skimage_na… 

    …pari

Improve median_filter_skimage_napari.py
    @tischi
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  7. Merge pull request #673 from NEUBIAS/improve_filter_variance_skimage_… 

    …napari.py

simplify filter_variance_skimage_napari.py
    @tischi
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  8. improve measure_intensities_act1_skimage_napari.py

    @tischi
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  9. Merge branch 'master' of https://github.com/NEUBIAS/training-resources

    @tischi
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  10. edited activity for '2D noisy object segmentation and filtering'

    akhan committed May 6, 2024
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  11. edited activity for '2D noisy object segmentation and filtering'

    akhan committed May 6, 2024
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  12. edited activity for '2D noisy object segmentation and filtering'

    akhan committed May 6, 2024
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  13. edited activity for '2D noisy object segmentation and filtering'

    akhan committed May 6, 2024
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  14. edited activity for '2D noisy object segmentation and filtering'

    akhan committed May 6, 2024
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  15. edited caption for main figure of 'Morphological filters'

    akhan committed May 6, 2024
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  16. edited caption for main figure of 'Morphological filters'

    akhan committed May 6, 2024
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Commits on May 7, 2024

  1. Several small fixes for python code for a couple of modules

    @tischi
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  2. Improve filter_morphological_act1_skimage_napari.py

    @tischi
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  3. fixed python code for activity 3 of 'Morphological filters'

    akhan committed May 7, 2024
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  4. fixed python code for activity 3 of 'Morphological filters'

    akhan committed May 7, 2024
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  5. Improve filter_morphological_act1_skimage_napari.py

    @tischi
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  6. Merge branch 'master' of https://github.com/NEUBIAS/training-resources

    @tischi
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  7. Add missing import to filter_morphological_act1_skimage_napari.py

    @tischi
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Commits on May 13, 2024

  1. Add filter_morphological/cytoplasmic_ring_skimage_napari.py; see #678

    @tischi
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Commits on May 14, 2024

  1. Comment out the napari.run() comment as this likely hangs the testing

    @tischi
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Commits on May 15, 2024

  1. Fixes #670

    @tischi
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Commits on May 16, 2024

  1. Fixes #681, hopefully cannot build website locally right now...

    @tischi
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  2. Improve string concat, fixes #682

    @tischi
    tischi committed May 16, 2024
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  3. Now add anything...

    @tischi
    tischi committed May 16, 2024
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  4. Fixes #680

    @tischi
    tischi committed May 16, 2024
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  5. Improve batch processing figure

    @tischi
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  6. Merge branch 'master' into issue659

    @tischi
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  7. WIP #569

    @tischi
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Commits on May 17, 2024

  1. Further work on #659

    @tischi
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  2. Implement binary image datatype activity for skimage napari:

    @tischi
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  3. Add template for batch analysis course

    @tischi
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  4. Improve YYYY_MM_HOST_automated_batch_analysis_python.md

    @tischi
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Commits on May 22, 2024

  1. Clean up inspect_8bit_saturation_skimage_napari.py

    @tischi
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Commits on May 27, 2024

  1. added skimage-napari-beginner course document for 07/2024

    @jhennies
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  2. fix windows ci (#675) 

    ci on windows would suddenly not find pytest executable
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Commits on May 28, 2024

  1. Remove iinfo for bool array (#687) 

    np.iinfo is not implemented for bool type (yet).

xref: numpy/numpy#8849
    @k-dominik
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  2. Added basic implementation for string and path manipulation in python

    @k-dominik
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  3. review suggestions 

    * group code sections with `# %%` (will be separate cells in notebooks)
* more meaningful comments

Co-authored-by: Christian Tischer <christian.tischer@embl.de>
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  4. Add more types of path manipulations to python activity

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  5. updated path manipulation, ijm 

    Updated with composing of new file names based on the python ex.

Also removed use of File.separator as getDirectory already returns a
trailing separator (at least on mac).
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  6. Merge pull request #686 from NEUBIAS/add-py-strings-paths 

    Added basic implementation for string and path manipulation in python
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  7. Rename 2024_07_idip-heidelberg_skimage_napari_beginners.md to 2024_07… 

    …_IDIP-Heidelberg_skimage_napari_beginners.md
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Commits on Jun 5, 2024

  1. Create 20240612_Goettingen_RTG_CYTAC.md

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  2. Update 20240612_Goettingen_RTG_CYTAC.md

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  3. Update 20240612_Goettingen_RTG_CYTAC.md

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  4. Update 20240612_Goettingen_RTG_CYTAC.md

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  5. Update 20240612_Goettingen_RTG_CYTAC.md

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  6. Update 20240612_Goettingen_RTG_CYTAC.md

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  7. add GBI-LNMA2024 course for Fiji

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  8. Update 20240612_Goettingen_RTG_CYTAC.md

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  9. Update 20240612_Goettingen_RTG_CYTAC.md

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  10. Update 20240612_Goettingen_RTG_CYTAC.md

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  11. Update YYYY_MM_HOST_automated_batch_analysis_python.md

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Commits on Jun 11, 2024

  1. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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  2. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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  3. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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  1. Update 20240612_Goettingen_RTG_CYTAC.md

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  2. Update 20240612_Goettingen_RTG_CYTAC.md

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  1. Update 20240612_Goettingen_RTG_CYTAC.md

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  2. Update 20240612_Goettingen_RTG_CYTAC.md

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Commits on Jun 20, 2024

  1. Merge branch 'master' of https://github.com/NEUBIAS/training-resources

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  2. init TIFF module

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Commits on Jun 24, 2024

  1. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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  1. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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  2. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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  3. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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  4. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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  5. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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  6. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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  7. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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Commits on Jun 26, 2024

  1. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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  2. Merge branch 'master' of https://github.com/NEUBIAS/training-resources

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Commits on Jun 27, 2024

  1. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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  2. Improve Coding with LLMs

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  3. Merge branch 'master' of https://github.com/NEUBIAS/training-resources

    @tischi
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  4. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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Commits on Jun 28, 2024

  1. Fix Chat-GPT link 

    Fix broken Chat-GPT link found during ZIDAS tutorial
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  2. Merge pull request #695 from jluethi/master 

    Fix Chat-GPT link
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Commits on Jun 29, 2024

  1. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md 

    Fix aesthetics
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Commits on Jun 30, 2024

  1. Datatypes WIP

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  2. Merge branch 'master' of https://github.com/NEUBIAS/training-resources

    @tischi
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  3. Implement 12 bit saturation activity for datatypes module

    @tischi
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  4. Improve projections skimage implementation

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  5. Further improve the projections skimage napari implementation

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Commits on Jul 1, 2024

  1. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

    @SeverinaKlaus
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  2. draft combined tutorial

    @martinschorb
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  3. Improve projections skimage implementation

    @tischi
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  4. more background info

    @martinschorb
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  5. Add image registration module skeleton

    @tischi
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  6. Improve spatial calibration skimage activity

    @tischi
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  7. Fix bug in new module creation script

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Commits on Jul 2, 2024

  1. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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  1. Merge branch 'refs/heads/master' into mobieCLEM

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  1. Address #669, #668, #667

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  2. Add scaling to shape measurements activity

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  1. Amend course schedule

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  2. Update workflow

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  3. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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  4. CLEM registration

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  5. Update filter_variance_skimage_napari.py

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  6. Implement python batch processing

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  7. Remove analysis result files

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  8. Merge branch 'master' of https://github.com/NEUBIAS/training-resources

    @tischi
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  9. Improve batch analysis module

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Commits on Jul 9, 2024

  1. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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  2. Update 2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

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Commits on Jul 11, 2024

  1. course protocol

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  2. Merge branch 'refs/heads/mobieCLEM'

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  1. svg not yet supported, replace by png

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  2. fix image link

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  3. typos

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Commits on Jul 18, 2024

  1. Changing variable name for output directory outside of the function

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  2. Saving data with save_ij_tiff for compatibility with open_ij_tiff; 

    Plotting first output image
    @jhennies
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  3. Updated batch processing description

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Commits on Jul 25, 2024

  1. Add 2024_08_EMBL_automated_batch_analysis_python.md

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  2. Merge pull request #706 from NEUBIAS/batch_processing 

    Updates for batch processing
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  3. Create python script which covers how to load images and read their m… 

    …etadata, as well as saves them again
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  4. Add python activity to module image file formats

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  5. Add little excersie block

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  6. Merge pull request #707 from felixS27/ImageFileFormatPython 

    Image file format python script (see #705)
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  1. merge

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  2. Merge branch 'master' into tiff

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Commits on Jul 29, 2024

  1. updated skimage napari conda environment creation instructions to to … 

    …exclude default channel in 'install_skimage_napari_conda.md'
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  2. Enable opening of activity implementations in URL

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  3. Merge branch 'master' of https://github.com/NEUBIAS/training-resources

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  4. Update 2024_08_EMBL_automated_batch_analysis_python.md

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Commits on Jul 30, 2024

  1. clean up courses folder a bit

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  2. Update 2024_08_EMBL_automated_batch_analysis_python.md 

    Corrected my name in the markdown
    @felixS27
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  3. Create notebook for teaching for loops in python

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  4. Add activity in modules

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  5. Zip archive containing the input images

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  6. MoBIE table for batch processing results

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  7. Removed Napari import

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  8. All measurement results to a single MoBIE-readable csv

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  9. Merge pull request #712 from NEUBIAS/forloops 

    Notebook to teach for loops in python
    @tischi
    tischi authored Jul 30, 2024
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  10. Removed python-dependent code from general activities

    @jhennies
    jhennies committed Jul 30, 2024
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  11. Changed link for ImageDataExplorer to publication

    @jhennies
    jhennies committed Jul 30, 2024
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  12. Merge pull request #713 from NEUBIAS/batch_processing 

    Batch processing
    @tischi
    tischi authored Jul 30, 2024
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  13. Shorten script to only include opening files

    @felixS27
    felixS27 committed Jul 30, 2024
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Commits on Jul 31, 2024

  1. Merge pull request #714 from NEUBIAS/710-remove-ome-tiff-saving-from-… 

    …first-image-file-formats-activity

Shorten script to only include opening files
    @tischi
    tischi authored Jul 31, 2024
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  2. added figure to 'script_functions.md'

    akhan committed Jul 31, 2024
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  3. improved 'script_functions' module

    akhan committed Jul 31, 2024
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Commits on Aug 1, 2024

  1. Fix recently introduced bug that would not allow to open certain acti… 

    …vities
    @tischi
    tischi committed Aug 1, 2024
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  2. merge

    @tischi
    tischi committed Aug 1, 2024
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  3. Reviewed 'script_functions' module according to Tischi's comments

    akhan committed Aug 1, 2024
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Commits on Aug 2, 2024

  1. Merge branch 'master' into galaxy

    @sunyi000
    sunyi000 committed Aug 2, 2024
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  2. Merge pull request #643 from NEUBIAS/galaxy 

    add instructions for the Galaxy platform
    @tischi
    tischi authored Aug 2, 2024
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  3. WIP

    @tischi
    tischi committed Aug 2, 2024
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Commits on Aug 5, 2024

  1. improve course

    @tischi
    tischi committed Aug 5, 2024
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  2. Merge branch 'master' of https://github.com/NEUBIAS/training-resources

    @tischi
    tischi committed Aug 5, 2024
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  3. Update 2024_08_EMBL_automated_batch_analysis_python.md

    @tischi
    tischi authored Aug 5, 2024
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  4. Update install_skimage_napari_conda.md

    @k-dominik
    k-dominik authored Aug 5, 2024
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  5. Improve module for scripting a function

    @tischi
    tischi committed Aug 5, 2024
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  6. Merge branch 'master' of https://github.com/NEUBIAS/training-resources

    @tischi
    tischi committed Aug 5, 2024
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Commits on Aug 6, 2024

  1. Update batch_measure_nuclei_shapes.md

    @jhennies
    jhennies authored Aug 6, 2024
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  2. Update batch_measure_nuclei_shapes.md

    @jhennies
    jhennies authored Aug 6, 2024
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  3. Update 2024_08_EMBL_automated_batch_analysis_python.md

    @tischi
    tischi authored Aug 6, 2024
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Commits on Aug 7, 2024

  1. Image data formats course WIP

    @tischi
    tischi committed Aug 7, 2024
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  2. Fix merge

    @tischi
    tischi committed Aug 7, 2024
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  3. Implement image data course draft

    @tischi
    tischi committed Aug 7, 2024
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  4. Merge branch 'master' of https://github.com/NEUBIAS/training-resources

    @tischi
    tischi committed Aug 7, 2024
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  5. Update 2024_??_EMBL_image_data_formats.md

    @tischi
    tischi authored Aug 7, 2024
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Commits on Aug 8, 2024

  1. Update 2024_??_EMBL_image_data_formats.md

    @tischi
    tischi authored Aug 8, 2024
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  2. Update README.md

    @tischi
    tischi authored Aug 8, 2024
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Commits on Sep 8, 2024

  1. Add acitivity to open CZI image, #720

    @tischi
    tischi committed Sep 8, 2024
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  2. Add acitivity to open TIFF series, #720

    @tischi
    tischi committed Sep 8, 2024
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Commits on Sep 16, 2024

  1. diverse improvements of image data modules

    @tischi
    tischi committed Sep 16, 2024
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Commits on Sep 17, 2024

  1. "Add activity to open CZI image refactored, #720"

    @felixS27
    felixS27 committed Sep 17, 2024
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  2. "Add activity to open CZI image refactored 2, #720"

    @felixS27
    felixS27 committed Sep 17, 2024
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  3. "Add activity to open LIF image, #720"

    @felixS27
    felixS27 committed Sep 17, 2024
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  4. "Add activity to open LIF image update, #720"

    @felixS27
    felixS27 committed Sep 17, 2024
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  5. "Add activity to open TIF image, #720"

    @felixS27
    felixS27 committed Sep 17, 2024
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  6. "Add activity to open TIFF series image, #720"

    @felixS27
    felixS27 committed Sep 17, 2024
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  7. "Add activity to open TIFF series image swap name, #720"

    @felixS27
    felixS27 committed Sep 17, 2024
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  8. Split script into beginner and advanced, #716

    @felixS27
    felixS27 committed Sep 17, 2024
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  9. Add activity #716

    @felixS27
    felixS27 committed Sep 17, 2024
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Commits on Sep 23, 2024

  1. Add ome_zarr_open_java.md

    @tischi
    tischi committed Sep 23, 2024
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  2. Merge branch 'master' of https://github.com/NEUBIAS/training-resources

    @tischi
    tischi committed Sep 23, 2024
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  3. Update OME-Zarr MoBIE implementation

    @tischi
    tischi committed Sep 23, 2024
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Commits on Sep 25, 2024

  1. Improve TIFF figure

    @tischi
    tischi committed Sep 25, 2024
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