Index

Symbols

--aligned-images spatialdata_io-xenium command line option --anndata-kwargs spatialdata_io-visium-hd command line option --anndata-path spatialdata_io-dbit command line option --annotate-table-by-labels spatialdata_io-visium-hd command line option --backend spatialdata_io-merscope command line option --barcode-position spatialdata_io-dbit command line option --bin-size spatialdata_io-visium-hd command line option --bins-as-squares spatialdata_io-visium-hd command line option --border spatialdata_io-dbit command line option --border-scale spatialdata_io-dbit command line option --c-chunks-size spatialdata_io-macsima command line option --c-subset spatialdata_io-macsima command line option --cells-as-circles spatialdata_io-seqfish command line option spatialdata_io-xenium command line option --cells-boundaries spatialdata_io-merscope command line option spatialdata_io-xenium command line option --cells-labels spatialdata_io-xenium command line option --cells-table spatialdata_io-merscope command line option spatialdata_io-xenium command line option --coordinate-system spatialdata_io-generic command line option --counts-file spatialdata_io-visium command line option --data-axes spatialdata_io-generic command line option --dataset-id spatialdata_io-cosmx command line option spatialdata_io-dbit command line option spatialdata_io-iss command line option spatialdata_io-stereoseq command line option spatialdata_io-visium command line option spatialdata_io-visium-hd command line option --default-scale-factor spatialdata_io-macsima command line option --fcs spatialdata_io-codex command line option --filter-folder-names spatialdata_io-macsima command line option --filtered-counts-file spatialdata_io-visium-hd command line option --fullres-image-file spatialdata_io-visium command line option spatialdata_io-visium-hd command line option --gex-only spatialdata_io-visium-hd command line option spatialdata_io-xenium command line option --h5ad-relative-path spatialdata_io-iss command line option --image-models-kwargs spatialdata_io-cosmx command line option spatialdata_io-iss command line option spatialdata_io-mcmicro command line option spatialdata_io-merscope command line option spatialdata_io-steinbock command line option spatialdata_io-stereoseq command line option spatialdata_io-visium command line option spatialdata_io-visium-hd command line option spatialdata_io-xenium command line option --image-path spatialdata_io-dbit command line option --imread-kwargs spatialdata_io-codex command line option spatialdata_io-cosmx command line option spatialdata_io-iss command line option spatialdata_io-macsima command line option spatialdata_io-mcmicro command line option spatialdata_io-merscope command line option spatialdata_io-seqfish command line option spatialdata_io-steinbock command line option spatialdata_io-stereoseq command line option spatialdata_io-visium command line option spatialdata_io-visium-hd command line option spatialdata_io-xenium command line option --include-cycle-in-channel-name spatialdata_io-macsima command line option --input spatialdata_io-codex command line option spatialdata_io-cosmx command line option spatialdata_io-curio command line option spatialdata_io-dbit command line option spatialdata_io-generic command line option spatialdata_io-iss command line option spatialdata_io-macsima command line option spatialdata_io-mcmicro command line option spatialdata_io-merscope command line option spatialdata_io-seqfish command line option spatialdata_io-steinbock command line option spatialdata_io-stereoseq command line option spatialdata_io-visium command line option spatialdata_io-visium-hd command line option spatialdata_io-xenium command line option --instance-key spatialdata_io-iss command line option --labels-kind spatialdata_io-steinbock command line option --labels-models-kwargs spatialdata_io-iss command line option spatialdata_io-mcmicro command line option spatialdata_io-xenium command line option --labels-relative-path spatialdata_io-iss command line option --load-all-images spatialdata_io-visium-hd command line option --load-images spatialdata_io-seqfish command line option --load-labels spatialdata_io-seqfish command line option

--load-nucleus-segmentations spatialdata_io-visium-hd command line option --load-points spatialdata_io-seqfish command line option --load-segmentations-only spatialdata_io-visium-hd command line option --load-shapes spatialdata_io-seqfish command line option --max-chunk-size spatialdata_io-macsima command line option --morphology-focus spatialdata_io-xenium command line option --morphology-mip spatialdata_io-xenium command line option --mosaic-images spatialdata_io-merscope command line option --multiscale spatialdata_io-macsima command line option --multiscale-image spatialdata_io-iss command line option --multiscale-labels spatialdata_io-iss command line option --name spatialdata_io-generic command line option --nuclei-channel-name spatialdata_io-macsima command line option --nucleus-boundaries spatialdata_io-xenium command line option --nucleus-labels spatialdata_io-xenium command line option --optional-tif spatialdata_io-stereoseq command line option --output spatialdata_io-codex command line option spatialdata_io-cosmx command line option spatialdata_io-curio command line option spatialdata_io-dbit command line option spatialdata_io-generic command line option spatialdata_io-iss command line option spatialdata_io-macsima command line option spatialdata_io-mcmicro command line option spatialdata_io-merscope command line option spatialdata_io-seqfish command line option spatialdata_io-steinbock command line option spatialdata_io-stereoseq command line option spatialdata_io-visium command line option spatialdata_io-visium-hd command line option spatialdata_io-xenium command line option --parsing-style spatialdata_io-macsima command line option --raster-models-scale-factors spatialdata_io-seqfish command line option --raw-relative-path spatialdata_io-iss command line option --read-square-bin spatialdata_io-stereoseq command line option --region-name spatialdata_io-merscope command line option --rois spatialdata_io-seqfish command line option --scale-factors spatialdata_io-macsima command line option --scalefactors-file spatialdata_io-visium command line option --skip-rounds spatialdata_io-macsima command line option --slide-name spatialdata_io-merscope command line option --split-threshold-nuclei-channel spatialdata_io-macsima command line option --subset spatialdata_io-macsima command line option --tissue-positions-file spatialdata_io-visium command line option --transcripts spatialdata_io-cosmx command line option spatialdata_io-merscope command line option spatialdata_io-xenium command line option --transformations spatialdata_io-macsima command line option --var-names-make-unique spatialdata_io-visium command line option spatialdata_io-visium-hd command line option --vpt-outputs spatialdata_io-merscope command line option --z-layers spatialdata_io-merscope command line option -c spatialdata_io-generic command line option -i spatialdata_io-codex command line option spatialdata_io-cosmx command line option spatialdata_io-curio command line option spatialdata_io-dbit command line option spatialdata_io-generic command line option spatialdata_io-iss command line option spatialdata_io-macsima command line option spatialdata_io-mcmicro command line option spatialdata_io-merscope command line option spatialdata_io-seqfish command line option spatialdata_io-steinbock command line option spatialdata_io-stereoseq command line option spatialdata_io-visium command line option spatialdata_io-visium-hd command line option spatialdata_io-xenium command line option -n spatialdata_io-generic command line option -o spatialdata_io-codex command line option spatialdata_io-cosmx command line option spatialdata_io-curio command line option spatialdata_io-dbit command line option spatialdata_io-generic command line option spatialdata_io-iss command line option spatialdata_io-macsima command line option spatialdata_io-mcmicro command line option spatialdata_io-merscope command line option spatialdata_io-seqfish command line option spatialdata_io-steinbock command line option spatialdata_io-stereoseq command line option spatialdata_io-visium command line option spatialdata_io-visium-hd command line option spatialdata_io-xenium command line option

C

codex() (in module spatialdata_io)

cosmx() (in module spatialdata_io) curio() (in module spatialdata_io)

D

dbit() (in module spatialdata_io)

F

from_legacy_anndata() (in module spatialdata_io.experimental)

G

generic() (in module spatialdata_io)

geojson() (in module spatialdata_io)

I

image() (in module spatialdata_io)

iss() (in module spatialdata_io.experimental)

M

mcmicro() (in module spatialdata_io) merscope() (in module spatialdata_io)

module spatialdata_io

S

seqfish() (in module spatialdata_io) spatialdata_io module spatialdata_io-codex command line option --fcs --imread-kwargs --input --output -i -o spatialdata_io-cosmx command line option --dataset-id --image-models-kwargs --imread-kwargs --input --output --transcripts -i -o spatialdata_io-curio command line option --input --output -i -o spatialdata_io-dbit command line option --anndata-path --barcode-position --border --border-scale --dataset-id --image-path --input --output -i -o spatialdata_io-generic command line option --coordinate-system --data-axes --input --name --output -c -i -n -o spatialdata_io-iss command line option --dataset-id --h5ad-relative-path --image-models-kwargs --imread-kwargs --input --instance-key --labels-models-kwargs --labels-relative-path --multiscale-image --multiscale-labels --output --raw-relative-path -i -o spatialdata_io-macsima command line option --c-chunks-size --c-subset --default-scale-factor --filter-folder-names --imread-kwargs --include-cycle-in-channel-name --input --max-chunk-size --multiscale --nuclei-channel-name --output --parsing-style --scale-factors --skip-rounds --split-threshold-nuclei-channel --subset --transformations -i -o spatialdata_io-mcmicro command line option --image-models-kwargs --imread-kwargs --input --labels-models-kwargs --output -i -o spatialdata_io-merscope command line option --backend --cells-boundaries --cells-table --image-models-kwargs --imread-kwargs --input --mosaic-images --output --region-name --slide-name --transcripts --vpt-outputs --z-layers -i -o

spatialdata_io-seqfish command line option --cells-as-circles --imread-kwargs --input --load-images --load-labels --load-points --load-shapes --output --raster-models-scale-factors --rois -i -o spatialdata_io-steinbock command line option --image-models-kwargs --imread-kwargs --input --labels-kind --output -i -o spatialdata_io-stereoseq command line option --dataset-id --image-models-kwargs --imread-kwargs --input --optional-tif --output --read-square-bin -i -o spatialdata_io-visium command line option --counts-file --dataset-id --fullres-image-file --image-models-kwargs --imread-kwargs --input --output --scalefactors-file --tissue-positions-file --var-names-make-unique -i -o spatialdata_io-visium-hd command line option --anndata-kwargs --annotate-table-by-labels --bin-size --bins-as-squares --dataset-id --filtered-counts-file --fullres-image-file --gex-only --image-models-kwargs --imread-kwargs --input --load-all-images --load-nucleus-segmentations --load-segmentations-only --output --var-names-make-unique -i -o spatialdata_io-xenium command line option --aligned-images --cells-as-circles --cells-boundaries --cells-labels --cells-table --gex-only --image-models-kwargs --imread-kwargs --input --labels-models-kwargs --morphology-focus --morphology-mip --nucleus-boundaries --nucleus-labels --output --transcripts -i -o steinbock() (in module spatialdata_io) stereoseq() (in module spatialdata_io)

T

to_legacy_anndata() (in module spatialdata_io.experimental)

V

visium() (in module spatialdata_io)

visium_hd() (in module spatialdata_io)

X

xenium() (in module spatialdata_io)

xenium_aligned_image() (in module spatialdata_io) xenium_explorer_selection() (in module spatialdata_io)