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fmi-faim / faim-ipa Public

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Make objects for plate and well acquisitions#59

Merged

tibuch merged 48 commits intomainfmi-faim/faim-ipa:mainfrom dev-janfmi-faim/faim-ipa:dev-janCopy head branch name to clipboard

Dec 13, 2023

+3,822-4,814

Conversation Commits48 (48)Checks Files changed

Commits

Commits on Dec 13, 2023

[wip] Make objects for plate and well acquisitions

imagejan
authored and
tibuch
committed
[wip]

imagejan
authored and
tibuch
committed
Harmonize tile-stitching and parsing.
tibuch
committed
[wip] Introduce Separate class to align tiles.
tibuch
committed
Create individual acquistion types and change use "ImageXpress Micro X" (Y, Z) instead of stage position.
tibuch
committed
Add optional background and illumination correction to tile data loading.
tibuch
committed
Fix division by zero warning.
tibuch
committed
Add convenience imports.
tibuch
committed
Add NGFF plate converter.
tibuch
committed
Add cellvoyager and roitable package.
tibuch
committed
Fix import order.
tibuch
committed
Fix enum type.
tibuch
committed
Load background and illumination correction matrices only once they are needed.
tibuch
committed
Add custom chunk-size in (z, y, x) and option to bin in yx.
tibuch
committed
Refactor run method.
tibuch
committed
Refactor.
tibuch
committed
Rework abstraction levels.
tibuch
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Add CellVoyagerWellAcquisition.
tibuch
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* Add omero channel metadata.
tibuch
committed
Update tests.
tibuch
committed
Limit number of threads in warping.
tibuch
committed
Fixed well shape for all wells.
tibuch
committed
Copy tile instead of creating a new one.
tibuch
committed
Add linear fusion function and fix warnings.
tibuch
committed
Test custom implementation.
tibuch
committed
Get dtype from WellAcquistion.
tibuch
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Warp mask and data together.
tibuch
committed
Refactor converter.
tibuch
committed
Refactor maximum well size computation.
tibuch
committed
Add Fractal ROI table functions which consume Plate/Well-Acquisition.
tibuch
committed
Refactor ChannelMetadata.
tibuch
committed
Refactor.
tibuch
committed
Update alignment test.
tibuch
committed
Add CellVoyagerWellAcquisition test.
tibuch
committed
Add cell voyager stack acquisition test.
tibuch
committed
Add ImageXpress tests.
tibuch
committed
Add plate and tests for plate.
tibuch
committed
Add tests for acquisition.
tibuch
committed
fix
tibuch
committed
Add converter tests.
tibuch
committed
Add Fractal ROI table tests.
tibuch
committed
Update tile tests.
tibuch
committed
Complete tests for stitching utils.
tibuch
committed
Add test for not implemented exceptions in abstract class.
tibuch
committed
Remove outdated code.
tibuch
committed
Replace jupyter notebooks with example scripts.
tibuch
committed
Add doc-strings.
tibuch
committed
Move visiview demo to visiview-stitching branch.
tibuch
committed

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