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timtreisand others added 4 commits March 31, 2025 23:32
@timtreis
added visium
c22b131
@timtreis
removed error
b943e01
@timtreis
refactor(tutorial): rewrite cp_measure notebook for merged SpatialDat…
20cb0e6
…a API
Rebuild tutorial_cpmeasure against sq.experimental.im.calculate_image_features
(SpatialData-native, per-object). Two parts: single-cell profiling on the
Xenium cells() dataset, and region profiling on Visium H&E spots. Drops the
pre-merge sketch (sq.exp, measurements=, cpmeasure:* flags, local zarr) and the
committed outputs; outputs are regenerated against the released squidpy.
Add tutorial_cpmeasure to the tutorials index.
@timtreis
test(tutorial): execute cp_measure notebook, commit outputs
f5b15df
Run end-to-end against the dev build and commit rendered outputs (5 figures).
Fixes found during execution:
- pass scale='scale0' to the morphology-only call (cell_labels is multiscale)
- drop non-finite feature columns before AND after scaling (float32 variance
underflow on near-constant columns nulls a column, breaking PCA)
- %matplotlib inline + warnings suppression for a clean rendered gallery
Outputs are from the dev build; they will be regenerated against the released
squidpy per the deploy plan.
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Add notebook illustration cp-measure based featurisation by timtreis · Pull Request #143 · scverse/squidpy-tutorials · GitHub
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timtreisand others
added 4 commits
March 31, 2025 23:32
@timtreis
added visium
c22b131
@timtreis
removed error
b943e01
@timtreis
refactor(tutorial): rewrite cp_measure notebook for merged SpatialDat…
20cb0e6
…a API
Rebuild tutorial_cpmeasure against sq.experimental.im.calculate_image_features
(SpatialData-native, per-object). Two parts: single-cell profiling on the
Xenium cells() dataset, and region profiling on Visium H&E spots. Drops the
pre-merge sketch (sq.exp, measurements=, cpmeasure:* flags, local zarr) and the
committed outputs; outputs are regenerated against the released squidpy.
Add tutorial_cpmeasure to the tutorials index.
@timtreis
test(tutorial): execute cp_measure notebook, commit outputs
f5b15df
Run end-to-end against the dev build and commit rendered outputs (5 figures).
Fixes found during execution:
- pass scale='scale0' to the morphology-only call (cell_labels is multiscale)
- drop non-finite feature columns before AND after scaling (float32 variance
underflow on near-constant columns nulls a column, breaking PCA)
- %matplotlib inline + warnings suppression for a clean rendered gallery
Outputs are from the dev build; they will be regenerated against the released
squidpy per the deploy plan.
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Add notebook illustration cp-measure based featurisation by timtreis · Pull Request #143 · scverse/squidpy-tutorials · GitHub
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Add notebook illustration cp-measure based featurisation - #143
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timtreisand others
added 4 commits
March 31, 2025 23:32
@timtreis
added visium
c22b131
@timtreis
removed error
b943e01
@timtreis
refactor(tutorial): rewrite cp_measure notebook for merged SpatialDat…
20cb0e6
…a API
Rebuild tutorial_cpmeasure against sq.experimental.im.calculate_image_features
(SpatialData-native, per-object). Two parts: single-cell profiling on the
Xenium cells() dataset, and region profiling on Visium H&E spots. Drops the
pre-merge sketch (sq.exp, measurements=, cpmeasure:* flags, local zarr) and the
committed outputs; outputs are regenerated against the released squidpy.
Add tutorial_cpmeasure to the tutorials index.
@timtreis
test(tutorial): execute cp_measure notebook, commit outputs
f5b15df
Run end-to-end against the dev build and commit rendered outputs (5 figures).
Fixes found during execution:
- pass scale='scale0' to the morphology-only call (cell_labels is multiscale)
- drop non-finite feature columns before AND after scaling (float32 variance
underflow on near-constant columns nulls a column, breaking PCA)
- %matplotlib inline + warnings suppression for a clean rendered gallery
Outputs are from the dev build; they will be regenerated against the released
squidpy per the deploy plan.
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Add notebook illustration cp-measure based featurisation by timtreis · Pull Request #143 · scverse/squidpy-tutorials · GitHub
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Add notebook illustration cp-measure based featurisation - #143
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Add notebook illustration cp-measure based featurisation#143
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timtreisand others
added 4 commits
March 31, 2025 23:32
@timtreis
added visium
c22b131
@timtreis
removed error
b943e01
@timtreis
refactor(tutorial): rewrite cp_measure notebook for merged SpatialDat…
20cb0e6
…a API
Rebuild tutorial_cpmeasure against sq.experimental.im.calculate_image_features
(SpatialData-native, per-object). Two parts: single-cell profiling on the
Xenium cells() dataset, and region profiling on Visium H&E spots. Drops the
pre-merge sketch (sq.exp, measurements=, cpmeasure:* flags, local zarr) and the
committed outputs; outputs are regenerated against the released squidpy.
Add tutorial_cpmeasure to the tutorials index.
@timtreis
test(tutorial): execute cp_measure notebook, commit outputs
f5b15df
Run end-to-end against the dev build and commit rendered outputs (5 figures).
Fixes found during execution:
- pass scale='scale0' to the morphology-only call (cell_labels is multiscale)
- drop non-finite feature columns before AND after scaling (float32 variance
underflow on near-constant columns nulls a column, breaking PCA)
- %matplotlib inline + warnings suppression for a clean rendered gallery
Outputs are from the dev build; they will be regenerated against the released
squidpy per the deploy plan.
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Add notebook illustration cp-measure based featurisation by timtreis · Pull Request #143 · scverse/squidpy-tutorials · GitHub
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Add notebook illustration cp-measure based featurisation - #143
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timtreisand others
added 4 commits
March 31, 2025 23:32
@timtreis
added visium
c22b131
@timtreis
removed error
b943e01
@timtreis
refactor(tutorial): rewrite cp_measure notebook for merged SpatialDat…
20cb0e6
…a API
Rebuild tutorial_cpmeasure against sq.experimental.im.calculate_image_features
(SpatialData-native, per-object). Two parts: single-cell profiling on the
Xenium cells() dataset, and region profiling on Visium H&E spots. Drops the
pre-merge sketch (sq.exp, measurements=, cpmeasure:* flags, local zarr) and the
committed outputs; outputs are regenerated against the released squidpy.
Add tutorial_cpmeasure to the tutorials index.
@timtreis
test(tutorial): execute cp_measure notebook, commit outputs
f5b15df
Run end-to-end against the dev build and commit rendered outputs (5 figures).
Fixes found during execution:
- pass scale='scale0' to the morphology-only call (cell_labels is multiscale)
- drop non-finite feature columns before AND after scaling (float32 variance
underflow on near-constant columns nulls a column, breaking PCA)
- %matplotlib inline + warnings suppression for a clean rendered gallery
Outputs are from the dev build; they will be regenerated against the released
squidpy per the deploy plan.
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, 'i');
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try {
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Add notebook illustration cp-measure based featurisation by timtreis · Pull Request #143 · scverse/squidpy-tutorials · GitHub
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Add notebook illustration cp-measure based featurisation - #143
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timtreisand others
added 4 commits
March 31, 2025 23:32
@timtreis
added visium
c22b131
@timtreis
removed error
b943e01
@timtreis
refactor(tutorial): rewrite cp_measure notebook for merged SpatialDat…
20cb0e6
…a API
Rebuild tutorial_cpmeasure against sq.experimental.im.calculate_image_features
(SpatialData-native, per-object). Two parts: single-cell profiling on the
Xenium cells() dataset, and region profiling on Visium H&E spots. Drops the
pre-merge sketch (sq.exp, measurements=, cpmeasure:* flags, local zarr) and the
committed outputs; outputs are regenerated against the released squidpy.
Add tutorial_cpmeasure to the tutorials index.
@timtreis
test(tutorial): execute cp_measure notebook, commit outputs
f5b15df
Run end-to-end against the dev build and commit rendered outputs (5 figures).
Fixes found during execution:
- pass scale='scale0' to the morphology-only call (cell_labels is multiscale)
- drop non-finite feature columns before AND after scaling (float32 variance
underflow on near-constant columns nulls a column, breaking PCA)
- %matplotlib inline + warnings suppression for a clean rendered gallery
Outputs are from the dev build; they will be regenerated against the released
squidpy per the deploy plan.
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try {
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Add notebook illustration cp-measure based featurisation by timtreis · Pull Request #143 · scverse/squidpy-tutorials · GitHub
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timtreisand others
added 4 commits
March 31, 2025 23:32
@timtreis
added visium
c22b131
@timtreis
removed error
b943e01
@timtreis
refactor(tutorial): rewrite cp_measure notebook for merged SpatialDat…
20cb0e6
…a API
Rebuild tutorial_cpmeasure against sq.experimental.im.calculate_image_features
(SpatialData-native, per-object). Two parts: single-cell profiling on the
Xenium cells() dataset, and region profiling on Visium H&E spots. Drops the
pre-merge sketch (sq.exp, measurements=, cpmeasure:* flags, local zarr) and the
committed outputs; outputs are regenerated against the released squidpy.
Add tutorial_cpmeasure to the tutorials index.
@timtreis
test(tutorial): execute cp_measure notebook, commit outputs
f5b15df
Run end-to-end against the dev build and commit rendered outputs (5 figures).
Fixes found during execution:
- pass scale='scale0' to the morphology-only call (cell_labels is multiscale)
- drop non-finite feature columns before AND after scaling (float32 variance
underflow on near-constant columns nulls a column, breaking PCA)
- %matplotlib inline + warnings suppression for a clean rendered gallery
Outputs are from the dev build; they will be regenerated against the released
squidpy per the deploy plan.
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, 'i');
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Add notebook illustration cp-measure based featurisation by timtreis · Pull Request #143 · scverse/squidpy-tutorials · GitHub
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Add notebook illustration cp-measure based featurisation - #143
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add_cpmeasure_notebook
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Add notebook illustration cp-measure based featurisation#143
timtreis wants to merge 5 commits into
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add_cpmeasure_notebook
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timtreisand others
added 4 commits
March 31, 2025 23:32
@timtreis
added visium
c22b131
@timtreis
removed error
b943e01
@timtreis
refactor(tutorial): rewrite cp_measure notebook for merged SpatialDat…
20cb0e6
…a API
Rebuild tutorial_cpmeasure against sq.experimental.im.calculate_image_features
(SpatialData-native, per-object). Two parts: single-cell profiling on the
Xenium cells() dataset, and region profiling on Visium H&E spots. Drops the
pre-merge sketch (sq.exp, measurements=, cpmeasure:* flags, local zarr) and the
committed outputs; outputs are regenerated against the released squidpy.
Add tutorial_cpmeasure to the tutorials index.
@timtreis
test(tutorial): execute cp_measure notebook, commit outputs
f5b15df
Run end-to-end against the dev build and commit rendered outputs (5 figures).
Fixes found during execution:
- pass scale='scale0' to the morphology-only call (cell_labels is multiscale)
- drop non-finite feature columns before AND after scaling (float32 variance
underflow on near-constant columns nulls a column, breaking PCA)
- %matplotlib inline + warnings suppression for a clean rendered gallery
Outputs are from the dev build; they will be regenerated against the released
squidpy per the deploy plan.
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