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From MuData to SpatialData#319

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SarahOuologuem wants to merge 57 commits intomainDendrouLab/panpipes:mainfrom sarah_spatialDataDendrouLab/panpipes:sarah_spatialDataCopy head branch name to clipboard

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Commits on Oct 4, 2024

• create spatialdata visium

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  921126e

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• create spatialdata vizgen

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  43e0c1e

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Commits on Oct 8, 2024

• rename python file

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  c1e823a

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• adjust spatial loading for spatialData

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  e3d6f2e

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• adjust spatial loading for spatialData

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  07844b5

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• remove squidpy merfish parameters

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  2c92e9a

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• add parameter=None for vizgen

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  d198b11

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• change h5mu to zarr

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  2b4c01b

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Commits on Oct 15, 2024

• change from mudata to spatialdata

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  459d07f

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• write obs spatialdata

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  c3fd8d5

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Commits on Oct 22, 2024

• adjust filtering to spatialdata

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  b828166

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• exchange h5mu for zarr

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  a3251d7

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Commits on Oct 24, 2024

• bug fix

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  5851feb

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• change mudata to spatialdata

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  dc969bb

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• bug fix

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  8920cde

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• bug fix

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  f1ac785

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• bug fixes

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  cb16526

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Commits on Nov 7, 2024

• add vpt parameters

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  24f035a

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• add vpt output parameter

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Commits on Nov 11, 2024

• add xenium

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Commits on Nov 26, 2024

• adjust sample submission file

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  8ab1570

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• add spatialdata

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  f3b8747

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• change file name

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  1937c1a

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• adjust submission file

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  5d17214

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• change None to string

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  72f5d5b

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• rename data files

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  afd6378

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Commits on Dec 1, 2024

• add ingest merscope action

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  90ef6e6

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• test to pin squidpy version

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  5fef8cf

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Commits on Dec 17, 2024

• remove detected transcripts

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  1f33c41

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• remove squidpy version pin

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  2f4392c

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• remove unnecessary imports

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  cf4ff07

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• add ingest xenium action

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  124d849

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• add cells.zarr file

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  a79bc58

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• add morphology focus folder

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  218f437

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• adjust spatial preprocessing to spatialData

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  89a19bf

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• adjust file name

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  5fa72b0

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• xenium adjust figshare links

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  7e04d41

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Commits on Jan 14, 2025

• update from mudata to spatialdata

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  1e002b5

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• correct data type of reference

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  35d5ecb

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• adjust to spatialData

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  358da95

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Commits on Jan 20, 2025

• add tangram github action

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  857d043

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Commits on Jan 28, 2025

• pin spatialdata version

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  573fcc2

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• pin dask

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  e4564c5

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• remove outfile_spatial

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• add option to export gene by spot matrix

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  86fd9d4

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Commits on Feb 4, 2025

• adjust docs to SpatialData

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  7e8bcf1

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• change to SpatialData

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  463ba6f

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Commits on Feb 10, 2025

• update to spatialData

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  5cb183b

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• check if columns exist

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  96695cf

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• remove index

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  4d873f2

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• fix bug

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  39d3c57

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• use zip files

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  775e334

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• change function and parameter names

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  66890d4

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• decrease font size

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• add changes to changelog

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Commits on Feb 12, 2025

• update comment

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• update logging info

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