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Add reader for Stereo-seq files. #70

Merged
merged 54 commits into from
May 24, 2024
Merged

Add reader for Stereo-seq files. #70

merged 54 commits into from
May 24, 2024

Commits on Jul 18, 2023

  1. Add reader for Stereo-seq data

    @LLehner
    LLehner committed Jul 18, 2023
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Commits on Jul 19, 2023

  1. Fix init

    @LLehner
    LLehner committed Jul 19, 2023
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  2. Fix duplicate Key values

    @LLehner
    LLehner committed Jul 19, 2023
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  3. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Jul 19, 2023
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  4. Add Key value

    @LLehner
    LLehner committed Jul 19, 2023
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  5. Merge branch 'Stereo-seq_reader' of https://github.com/LLehner/spatia… 

    …ldata-io into Stereo-seq_reader
    @LLehner
    LLehner committed Jul 19, 2023
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Commits on Aug 3, 2023

  1. Add shapes

    @LLehner
    LLehner committed Aug 3, 2023
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  2. Remove print

    @LLehner
    LLehner committed Aug 3, 2023
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Commits on Aug 7, 2023

  1. Fix radius

    @LLehner
    LLehner committed Aug 7, 2023
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Commits on Aug 19, 2023

  1. Fix constants

    @LLehner
    LLehner committed Aug 19, 2023
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Commits on Aug 20, 2023

  1. Update constants and reader

    @LLehner
    LLehner committed Aug 20, 2023
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  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Aug 20, 2023
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  3. Fix constants

    @LLehner
    LLehner committed Aug 20, 2023
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  4. Add dataset identifier

    @LLehner
    LLehner committed Aug 20, 2023
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  5. Update reader

    @LLehner
    LLehner committed Aug 20, 2023
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  6. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
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    pre-commit-ci[bot] committed Aug 20, 2023
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  7. Fix parameters

    @LLehner
    LLehner committed Aug 20, 2023
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  8. Merge branch 'Stereo-seq_reader' of https://github.com/LLehner/spatia… 

    …ldata-io into Stereo-seq_reader
    @LLehner
    LLehner committed Aug 20, 2023
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  9. Fix parameters

    @LLehner
    LLehner committed Aug 20, 2023
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  10. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Aug 20, 2023
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  11. Fix input parameters

    @LLehner
    LLehner committed Aug 20, 2023
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  12. Merge branch 'Stereo-seq_reader' of https://github.com/LLehner/spatia… 

    …ldata-io into Stereo-seq_reader
    @LLehner
    LLehner committed Aug 20, 2023
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  13. Fix input parameters

    @LLehner
    LLehner committed Aug 20, 2023
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  14. Fix input parameters

    @LLehner
    LLehner committed Aug 20, 2023
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  15. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Aug 20, 2023
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  16. Fix mypy

    @LLehner
    LLehner committed Aug 20, 2023
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  17. Merge branch 'Stereo-seq_reader' of https://github.com/LLehner/spatia… 

    …ldata-io into Stereo-seq_reader
    @LLehner
    LLehner committed Aug 20, 2023
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  18. Fix input parameters

    @LLehner
    LLehner committed Aug 20, 2023
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Commits on Aug 21, 2023

  1. Fix mypy

    @LLehner
    LLehner committed Aug 21, 2023
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Commits on Feb 21, 2024

  1. Fix automatic dataset_id detection

    @LLehner
    LLehner committed Feb 21, 2024
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  2. Update cellbin_gef location and allow multiple mask files

    @LLehner
    LLehner committed Feb 21, 2024
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  3. Add optional read arguments

    @LLehner
    LLehner committed Feb 21, 2024
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  4. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Feb 21, 2024
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  5. Fix pre-commit

    @LLehner
    LLehner committed Feb 21, 2024
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  6. Merge branch 'Stereo-seq_reader' of https://github.com/LLehner/spatia… 

    …ldata-io into Stereo-seq_reader
    @LLehner
    LLehner committed Feb 21, 2024
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Commits on Feb 23, 2024

  1. Update cellbin_gef location

    @LLehner
    LLehner committed Feb 23, 2024
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Commits on Feb 26, 2024

  1. Fix duplicate key names in images and labels

    @LLehner
    LLehner committed Feb 26, 2024
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Commits on May 7, 2024

  1. Merge branch 'main' into Stereo-seq_reader

    @LucaMarconato
    LucaMarconato committed May 7, 2024
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  2. fix spelling

    @LucaMarconato
    LucaMarconato committed May 7, 2024
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  3. fixed cellID being nan due to incorrect assigned name

    @LucaMarconato
    LucaMarconato committed May 7, 2024
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Commits on May 15, 2024

  1. fix metadata

    @LucaMarconato
    LucaMarconato committed May 15, 2024
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Commits on May 16, 2024

  1. wip bin data parsing

    @LucaMarconato
    LucaMarconato committed May 16, 2024
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  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed May 16, 2024
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  3. renamed StereoseqKeys to SK

    @LucaMarconato
    LucaMarconato committed May 16, 2024
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  4. Merge branch 'Stereo-seq_reader' of https://github.com/LLehner/spatia… 

    …ldata-io into Stereo-seq_reader
    @LucaMarconato
    LucaMarconato committed May 16, 2024
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Commits on May 21, 2024

  1. comparing points vs shapes for bins

    @LucaMarconato
    LucaMarconato committed May 21, 2024
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  2. using points for bins

    @LucaMarconato
    LucaMarconato committed May 21, 2024
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Commits on May 22, 2024

  1. experiment with relabeling; I will remove the code

    @LucaMarconato
    LucaMarconato committed May 22, 2024
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  2. cleanup

    @LucaMarconato
    LucaMarconato committed May 22, 2024
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  3. fix spatialdata dependency

    @LucaMarconato
    LucaMarconato committed May 22, 2024
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Commits on May 24, 2024

  1. stereoseq fixes

    @LucaMarconato
    LucaMarconato committed May 24, 2024
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  2. changelog

    @LucaMarconato
    LucaMarconato committed May 24, 2024
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  3. add stereoseq to readme

    @LucaMarconato
    LucaMarconato committed May 24, 2024
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  4. cleanup

    @LucaMarconato
    LucaMarconato committed May 24, 2024
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