Mercurial > repos > iuc > spatialdata_io
view spatialdata_io.xml @ 0:1f6c780a2635 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/spatialdata commit 87bff76d897c5a4277d9987cf26432a18e0458cd-dirty
| author | iuc |
|---|---|
| date | Sat, 14 Mar 2026 15:16:08 +0000 |
| parents | |
| children |
line wrap: on
line source
<tool id="spatialdata_io" name="SpatialData IO" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>load common spatial omics formats into SpatialData</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="creator" /> <command detect_errors="exit_code"><![CDATA[ ## CosMX #if $method_condi.method == 'cosmx': ## puting all files in working directory instead of input. cosmx should run inside same directory mkdir -p 'CellComposite' 'CellLabels' 'output' && #for $image in $method_condi.CellComposite: #if $image.element_identifier.endswith('.jpg'): ln -s '$image' 'CellComposite/${image.element_identifier}' && #else: ln -s '$image' 'CellComposite/${image.element_identifier}.jpg' && #end if #end for #for $image in $method_condi.CellLabels: #if $image.element_identifier.endswith('.tiff') or $image.element_identifier.endswith('.tif'): ln -s '$image' 'CellLabels/${image.element_identifier}' && #else: ln -s '$image' 'CellLabels/${image.element_identifier}.tiff' && #end if #end for #if $method_condi.exprMat_file.element_identifier.endswith('.csv'): ln -s '$method_condi.exprMat_file' '${method_condi.exprMat_file.element_identifier}' && #else: ln -s '$method_condi.exprMat_file' '${method_condi.exprMat_file.element_identifier}.csv' && #end if #if $method_condi.fov_positions_file.element_identifier.endswith('.csv'): ln -s '$method_condi.fov_positions_file' '${method_condi.fov_positions_file.element_identifier}' && #else: ln -s '$method_condi.fov_positions_file' '${method_condi.fov_positions_file.element_identifier}.csv' && #end if #if $method_condi.metadata_file.element_identifier.endswith('.csv'): ln -s '$method_condi.metadata_file' '${method_condi.metadata_file.element_identifier}' && #else: ln -s '$method_condi.metadata_file' '${method_condi.metadata_file.element_identifier}.csv' && #end if #if $method_condi.tx_file.element_identifier.endswith('.csv'): ln -s '$method_condi.tx_file' '${method_condi.tx_file.element_identifier}' && #else: ln -s '$method_condi.tx_file' '${method_condi.tx_file.element_identifier}.csv' && #end if ## CURIO #else if $method_condi.method == 'curio': mkdir -p 'input' 'output' && ln -s '$method_condi.anndata' 'input/${method_condi.dataset_id}_anndata.h5ad' && ln -s '$method_condi.cluster_assignment' 'input/${method_condi.dataset_id}_cluster_assignment.txt' && ln -s '$method_condi.metrics' 'input/${method_condi.dataset_id}_Metrics.csv' && ln -s '$method_condi.variable_features_clusters' 'input/${method_condi.dataset_id}_variable_features_clusters.txt' && ln -s '$method_condi.variable_features_spatial' 'input/${method_condi.dataset_id}_variable_features_spatial_moransi.txt' && ## DBIT #else if $method_condi.method == 'dbit': ## puting all files in working directory instead of input. dbit should run inside same directory mkdir -p 'output' && ln -s '$method_condi.barcode_positions' '${method_condi.dataset_id}_barcode_positions.tabular' && ln -s '$method_condi.counts' '${method_condi.dataset_id}_counts.h5ad' && ln -s '$method_condi.tissue_lowres' '${method_condi.dataset_id}_tissue_lowres.png' && ## MACSima #else if $method_condi.method == 'macsima': mkdir -p 'input' 'output' && #for $image in $method_condi.tiff_files: #if $image.element_identifier.endswith('.tif') or $image.element_identifier.endswith('.tiff'): ln -s '$image' 'input/${image.element_identifier}' && #else: ln -s '$image' 'input/${image.element_identifier}.tif' && #end if #end for ## MERSCOPE #else if $method_condi.method == 'merscope': mkdir -p 'input/region/images' 'input/region/vpt_outputs' 'output' && #for $image in $method_condi.mosaic_images: #if $image.element_identifier.endswith('.tif'): ln -s '$image' 'input/region/images/${image.element_identifier}' && #else: ln -s '$image' 'input/region/images/${image.element_identifier}.tif' && #end if #end for ln -s '$method_condi.input_micron_to_mosaic' 'input/region/images/micron_to_mosaic_pixel_transform.csv' && ln -s '$method_condi.cell_by_gene' 'input/region/vpt_outputs/cell_by_gene.csv' && ln -s '$method_condi.cell_meta' 'input/region/vpt_outputs/cell_metadata.csv' && ## the tool checks the file name, so the name is hardcoded here, but it does not necessarily have to be from cellpose ln -s '$method_condi.cells_boundaries' 'input/region/vpt_outputs/cellpose_micron_space.parquet' && ln -s '$method_condi.transcripts' 'input/region/detected_transcripts.csv' && ## Visium #else if $method_condi.method == 'visium': mkdir -p 'input/spatial' 'output' && #if $method_condi.matrix_bool: ln -s '$method_condi.feature_bc_matrix' 'input/raw_feature_bc_matrix.h5' && #else: ln -s '$method_condi.feature_bc_matrix' 'input/filtered_feature_bc_matrix.h5' && #end if ln -s '$method_condi.scalefactors_json' 'input/scalefactors_json.json' && ln -s '$method_condi.fullres_image_file' 'input/fullres_image.tif' && ln -s '$method_condi.tissue_hires_image' 'input/spatial/tissue_hires_image.png' && ln -s '$method_condi.tissue_lowres_image' 'input/spatial/tissue_lowres_image.png' && ln -s '$method_condi.tissue_positions_list' 'input/tissue_positions_list.csv' && ## Visium HD #else if $method_condi.method == 'visium_hd': mkdir -p 'input' 'output' && ## Core required file ln -s '$method_condi.feature_slice' 'input/feature_slice.h5' && ## Binned outputs (if included) #if str($method_condi.include_binned_condi.include_binned) == 'yes': ## Bin 002um (required for nucleus segmentation if enabled) #if $method_condi.include_binned_condi.bin002.feature_bc_matrix_002: mkdir -p 'input/binned_outputs/square_002um/spatial' && #if $method_condi.matrix_bool: ln -s '$method_condi.include_binned_condi.bin002.feature_bc_matrix_002' 'input/binned_outputs/square_002um/raw_feature_bc_matrix.h5' && #else: ln -s '$method_condi.include_binned_condi.bin002.feature_bc_matrix_002' 'input/binned_outputs/square_002um/filtered_feature_bc_matrix.h5' && #end if ln -s '$method_condi.include_binned_condi.bin002.tissue_positions_002' 'input/binned_outputs/square_002um/spatial/tissue_positions.parquet' && ln -s '$method_condi.include_binned_condi.bin002.scalefactors_json_002' 'input/binned_outputs/square_002um/spatial/scalefactors_json.json' && #end if ## Bin 008um #if $method_condi.include_binned_condi.bin008.feature_bc_matrix_008: mkdir -p 'input/binned_outputs/square_008um/spatial' && #if $method_condi.matrix_bool: ln -s '$method_condi.include_binned_condi.bin008.feature_bc_matrix_008' 'input/binned_outputs/square_008um/raw_feature_bc_matrix.h5' && #else: ln -s '$method_condi.include_binned_condi.bin008.feature_bc_matrix_008' 'input/binned_outputs/square_008um/filtered_feature_bc_matrix.h5' && #end if ln -s '$method_condi.include_binned_condi.bin008.tissue_positions_008' 'input/binned_outputs/square_008um/spatial/tissue_positions.parquet' && ln -s '$method_condi.include_binned_condi.bin008.scalefactors_json_008' 'input/binned_outputs/square_008um/spatial/scalefactors_json.json' && #end if ## Bin 016um #if $method_condi.include_binned_condi.bin016.feature_bc_matrix_016: mkdir -p 'input/binned_outputs/square_016um/spatial' && #if $method_condi.matrix_bool: ln -s '$method_condi.include_binned_condi.bin016.feature_bc_matrix_016' 'input/binned_outputs/square_016um/raw_feature_bc_matrix.h5' && #else: ln -s '$method_condi.include_binned_condi.bin016.feature_bc_matrix_016' 'input/binned_outputs/square_016um/filtered_feature_bc_matrix.h5' && #end if ln -s '$method_condi.include_binned_condi.bin016.tissue_positions_016' 'input/binned_outputs/square_016um/spatial/tissue_positions.parquet' && ln -s '$method_condi.include_binned_condi.bin016.scalefactors_json_016' 'input/binned_outputs/square_016um/spatial/scalefactors_json.json' && #end if ## Nucleus segmentation (requires barcode_mappings at root) #if str($method_condi.include_binned_condi.include_nucleus_seg_condi.include_nucleus_seg) == 'yes': mkdir -p 'input/segmented_outputs/' && ln -s '$method_condi.include_binned_condi.include_nucleus_seg_condi.barcode_mappings' 'input/barcode_mappings.parquet' && ln -s '$method_condi.include_binned_condi.include_nucleus_seg_condi.nucleus_segmentation' 'input/segmented_outputs/nucleus_segmentations.geojson' && #end if #end if ## Segmented outputs (cell segmentation) #if str($method_condi.segmentation_conditional.enable_segmentation) == 'yes': mkdir -p 'input/segmented_outputs/spatial' && #if $method_condi.matrix_bool: ln -s '$method_condi.segmentation_conditional.feature_bc_matrix_seg' 'input/segmented_outputs/raw_feature_cell_matrix.h5' && #else: ln -s '$method_condi.segmentation_conditional.feature_bc_matrix_seg' 'input/segmented_outputs/filtered_feature_cell_matrix.h5' && #end if ln -s '$method_condi.segmentation_conditional.cell_segmentation' 'input/segmented_outputs/cell_segmentations.geojson' && ln -s '$method_condi.segmentation_conditional.scalefactors_json_seg' 'input/segmented_outputs/spatial/scalefactors_json.json' && #end if ## Images (placed in spatial/ and/or segmented_outputs/spatial/) mkdir -p 'input/spatial' && #if $method_condi.images.tissue_hires: ln -s '$method_condi.images.tissue_hires' 'input/spatial/tissue_hires_image.png' && #end if #if $method_condi.images.tissue_lowres: ln -s '$method_condi.images.tissue_lowres' 'input/spatial/tissue_lowres_image.png' && #end if #if str($method_condi.images.cytassist_image_condi.include_cytassist) == 'yes': ln -s '$method_condi.images.cytassist_image_condi.cytassist_image' 'input/spatial/cytassist_image.tiff' && #end if ## Microscope image (if provided, create microscope_image directory) #if $method_condi.images.microscope_image: mkdir -p 'input/microscope_image' && ln -s '$method_condi.images.microscope_image' 'input/microscope_image/fullres_image.tiff' && #end if echo "echoing the structure..." && tree -L 3 input && ## XENIUM #else if $method_condi.method == 'xenium': mkdir -p 'input/region/morphology_focus/' 'output' && ## ln -s does not work here. #if str($method_condi.cell_boundaries) != '': cp '$method_condi.cell_boundaries' 'input/region/cell_boundaries.parquet' && #end if cp '$method_condi.cell_feature_matrix' 'input/region/cell_feature_matrix.h5' && cp '$method_condi.cells' 'input/region/cells.parquet' && cp '$method_condi.cells_zarr' 'input/region/cells.zarr.zip' && cp '$method_condi.experiment_xenium' 'input/region/experiment.xenium' && #for $image in $method_condi.morphology_focus: #if $image.element_identifier.endswith('.ome.tiff') or $image.element_identifier.endswith('.ome.tif'): cp '$image' 'input/region/morphology_focus/${image.element_identifier}' && #else: cp '$image' 'input/region/morphology_focus/${image.element_identifier}.ome.tif' && #end if #end for #if str($method_condi.nucleus_boundaries) != '': cp '$method_condi.nucleus_boundaries' 'input/region/nucleus_boundaries.parquet' && #end if #if str($method_condi.transcripts) != '': cp '$method_condi.transcripts' 'input/region/transcripts.parquet' && #end if #if str($method_condi.add_hne_condi.add_hne) == 'yes' or str($method_condi.add_hne_condi.add_hne) == 'yes_accurate': cp '$method_condi.add_hne_condi.hne_image' 'input/region/he_image.ome.tif' && #end if #if str($method_condi.add_if_condi.add_if) == 'yes' or str($method_condi.add_if_condi.add_if) == 'yes_accurate': cp '$method_condi.add_if_condi.if_image' 'input/region/if_image.ome.tif' && #end if #if str($method_condi.add_hne_condi.add_hne) == 'yes_accurate': cp '$method_condi.add_hne_condi.image_alignment' 'input/region/he_image_alignment.csv' && #end if #if str($method_condi.add_if_condi.add_if) == 'yes_accurate': cp '$method_condi.add_if_condi.image_alignment' 'input/region/if_image_alignment.csv' && #end if #end if ## run the pipeline cat 'spdata_io.py' && python3 'spdata_io.py' && ## zip the output spatialdata folder cd output && zip -r ../spatialdata.spatialdata.zip spatialdata/ && cd .. ]]></command> <configfiles> <configfile name="spdata_config" filename="spdata_io.py"> #if $method_condi.method == 'cosmx': from spatialdata_io import cosmx spdata = cosmx(path="./", dataset_id="$method_condi.dataset_id", transcripts=$method_condi.transcripts_bool, ) #else if $method_condi.method == 'curio': from spatialdata_io import curio spdata = curio(path="./input" ) #else if $method_condi.method == 'dbit': from spatialdata_io import dbit spdata = dbit(path="./", anndata_path="${method_condi.dataset_id}_counts.h5ad", barcode_position="${method_condi.dataset_id}_barcode_positions.tabular", image_path="${method_condi.dataset_id}_tissue_lowres.png", dataset_id="$method_condi.dataset_id", border=$method_condi.border, border_scale=$method_condi.border_scale, ) #else if $method_condi.method == 'macsima': from spatialdata_io import macsima spdata = macsima(path="./input", parsing_style="auto", #if $method_condi.subset: subset=$method_condi.subset, #end if #if $method_condi.subset_c: subset_c=$method_condi.subset_c, #end if max_chunk_size=$method_condi.max_chunk_size, c_chunks_size=$method_condi.c_chunks_size, multiscale=$method_condi.multiscale_bool, transformations=$method_condi.transformations_bool, #if str($method_condi.scale_factors) != '': #set scale_factors_list = [int(x.strip()) for x in str($method_condi.scale_factors).split(',')] scale_factors=$scale_factors_list, #end if nuclei_channel_name="$method_condi.nuclei_channel_name", #if str($method_condi.split_threshold_nuclei_channel) != '': split_threshold_nuclei_channel=$method_condi.split_threshold_nuclei_channel, #else: split_threshold_nuclei_channel=None, #end if include_cycle_in_channel_name=$method_condi.include_cycle_in_channel_name_bool, ) #else if $method_condi.method == 'merscope': from spatialdata_io import merscope spdata = merscope(path="./input/region", vpt_outputs="./input/region/vpt_outputs", #set z_layers_list = [int(x.strip()) for x in str($method_condi.z_layers).split(',')] z_layers=$z_layers_list, region_name="$method_condi.region_name", slide_name="$method_condi.slide_name", backend="rioxarray", transcripts=$method_condi.transcripts_bool, cells_boundaries=$method_condi.cells_boundaries_bool, cells_table=$method_condi.cells_table_bool, mosaic_images=$method_condi.mosaic_images_bool, ) #else if $method_condi.method == 'visium': from spatialdata_io import visium spdata = visium(path="./input", dataset_id="$method_condi.dataset_id", #if $method_condi.matrix_bool: counts_file='raw_feature_bc_matrix.h5', #else: counts_file='filtered_feature_bc_matrix.h5', #end if fullres_image_file='fullres_image.tif', tissue_positions_file='tissue_positions_list.csv', scalefactors_file='scalefactors_json.json', var_names_make_unique=True, ) #else if $method_condi.method == 'visium_hd': from spatialdata_io import visium_hd spdata = visium_hd(path="./input", dataset_id="$method_condi.dataset_id", #if $method_condi.matrix_bool: filtered_counts_file=False, #else: filtered_counts_file=True, #end if #if str($method_condi.include_binned_condi.include_binned) == 'no': load_segmentations_only=True, #else: load_segmentations_only=False, #end if #if str($method_condi.include_binned_condi.include_binned) == 'yes' and str($method_condi.include_binned_condi.include_nucleus_seg_condi.include_nucleus_seg) == 'yes': load_nucleus_segmentations=True, #else: load_nucleus_segmentations=False, #end if bin_size=None, bins_as_squares=$method_condi.bins_as_squares_bool, annotate_table_by_labels=$method_condi.annotate_table_by_labels_bool, #if $method_condi.images.microscope_image: fullres_image_file="./input/microscope_image/fullres_image.tiff", #else: fullres_image_file=None, #end if #if str($method_condi.images.cytassist_image_condi.include_cytassist) == 'yes': load_all_images=True, #else: load_all_images=False, #end if var_names_make_unique=$method_condi.var_names_make_unique_bool, ) #else if $method_condi.method == 'xenium': import os from spatialdata_io import xenium spdata = xenium(path="./input/region", #if str($method_condi.cell_boundaries) != '': cells_boundaries=True, #else: cells_boundaries=False, #end if #if str($method_condi.nucleus_boundaries) != '': nucleus_boundaries=True, #else: nucleus_boundaries=False, #end if cells_as_circles=$method_condi.cells_as_circles_bool, cells_labels=$method_condi.cells_labels_bool, nucleus_labels=$method_condi.nucleus_labels_bool, #if str($method_condi.transcripts) != '': transcripts=True, #else: transcripts=False, #end if morphology_mip=$method_condi.morphology_mip_bool, morphology_focus=$method_condi.morphology_focus_bool, #if str($method_condi.add_hne_condi.add_hne) == 'yes' or str($method_condi.add_if_condi.add_if) == 'yes': aligned_images=True, #else: aligned_images=False, #end if cells_table=$method_condi.cells_table_bool, gex_only=$method_condi.gex_only_bool, n_jobs=int(os.getenv("GALAXY_SLOTS")), ) #if str($method_condi.add_if_condi.add_if) == 'yes_accurate': from spatialdata_io import xenium_aligned_image spdata["if_image"] = xenium_aligned_image( image_path="./input/region/if_image.ome.tif", alignment_file="./input/region/if_image_alignment.csv" ) #else if str($method_condi.add_hne_condi.add_hne) == 'yes_accurate': from spatialdata_io import xenium_aligned_image spdata["he_image"] = xenium_aligned_image( image_path="./input/region/he_image.ome.tif", alignment_file="./input/region/he_image_alignment.csv" ) #end if #end if print(spdata) spdata.write("./output/spatialdata", overwrite=True) </configfile> </configfiles> <inputs> <conditional name="method_condi"> <param name="method" type="select" label="Spatial Technology"> <option value="cosmx">CosMx</option> <option value="dbit">DBiT-seq</option> <option value="macsima">MACSima</option> <option value="merscope">MERSCOPE</option> <option value="visium">10x Genomics Visium</option> <option value="visium_hd">10x Genomics Visium HD</option> <option value="xenium">10x Genomics Xenium</option> </param> <when value="cosmx"> <param name="CellComposite" type="data" format="jpg,png,tiff" multiple="true" label="Cell Composite images"/> <param name="CellLabels" type="data" format="tiff" multiple="true" label="Cell Labels images"/> <param name="exprMat_file" type="data" format="csv" label="Expression matrix file"/> <param name="fov_positions_file" type="data" format="csv" label="FOV positions file"/> <param name="metadata_file" type="data" format="csv" label="Metadata file"/> <param name="tx_file" type="data" format="csv" label="Transcripts file"/> <param name="dataset_id" type="text" value="Galaxy" label="Dataset identifier" help="It should match your input files name"> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> <add value="_" /> </valid> </sanitizer> <validator type="regex">[0-9a-zA-Z_]+</validator> </param> <param name="transcripts_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load transcripts information?"/> </when> <when value="dbit"> <param name="barcode_positions" type="data" format="tabular" label="Barcode positions file"/> <param name="counts" type="data" format="h5ad" label="Counts file"/> <param name="tissue_lowres" type="data" format="png" label="Tissue low resolution image"/> <param name="dataset_id" type="text" value="Galaxy" label="Dataset identifier" help="It should match your input files name"> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> <add value="_" /> </valid> </sanitizer> <validator type="regex">[0-9a-zA-Z_]+</validator> </param> <param name="border" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Create a border" help="If True, the square is shrinked toward its center, leaving an empty border." /> <param name="border_scale" type="float" value="1" label="Border scale factor" help="The factor by which the border is scaled. The default is 1. It corresponds to a border length of (0.125 * length of the square’s edge)"/> </when> <when value="macsima"> <param name="tiff_files" type="data" format="tiff" multiple="true" label="MACSima TIFF images" help="OME-TIFF files from MACSima cyclic imaging experiment"/> <param name="subset" type="integer" min="0" optional="true" label="Subset the image to the first ``subset`` pixels in x and y dimensions"/> <param name="subset_c" type="integer" min="0" optional="true" label="Subset the image to the first ``c_subset`` channels"/> <param name="max_chunk_size" type="integer" min="0" value="1024" label="Maximum chunk size for x and y dimension"/> <param name="c_chunks_size" type="integer" min="0" value="1" label="Maximum chunk size for x and y dimension"/> <param name="multiscale_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Create multiscale image?"/> <param name="transformations_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to add a transformation from pixels to microns to the image"/> <param name="scale_factors" type="integer" min="0" optional="true" label="Scale factors to use for downsampling" help="If None, scale factors are calculated based on image size."/> <param name="nuclei_channel_name" type="text" value="DAPI" label="Nuclei channel name"/> <param name="split_threshold_nuclei_channel" type="integer" min="0" value="2" optional="true" label="Split threshold for nuclei channels" help="If the number of channels that include nuclei_channel_name is greater than this threshold, the nuclei channels are split into a separate stack.."/> <param name="include_cycle_in_channel_name_bool" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Include cycle number in channel name?" help="If True, prepend cycle number to channel names (e.g., 'R1 DAPI')"/> </when> <when value="merscope"> <param name="slide_name" type="text" value="Galaxy" label="Dataset identifier" help="Prefix used to name the constructed SpatialData elements."> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> <add value="_" /> </valid> </sanitizer> <validator type="regex">[0-9a-zA-Z_]+</validator> </param> <param name="region_name" type="text" value="region" label="Region name" help="Region name appended to the dataset identifier in the MERSCOPE output."> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> <add value="_" /> </valid> </sanitizer> <validator type="regex">[0-9a-zA-Z_]+</validator> </param> <param argument="--z_layers" type="text" value="3" optional="false" label="Comma separated list of Indices of the z-layers to consider" help="By default, only the middle layer is considered (layer 3)."> <expand macro="sanitize_digits"/> </param> <param argument="--mosaic-images" type="data" format="tiff" multiple="true" label="MEROSCOPE tiff images"/> <param name="input_micron_to_mosaic" type="data" format="csv" label="Micron to mosaic mapping file"/> <param name="cell_by_gene" type="data" format="csv" label="Cell by gene table" help="Cells as rows and Genes as columns"/> <param name="cell_meta" type="data" format="csv" label="Cell metadata table"/> <param name="cells_boundaries" type="data" format="parquet" label="Cell boundaries (micron_space)"/> <param name="transcripts" type="data" format="csv" label="Detected transcripts"/> <param name="transcripts_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load transcripts information?"/> <param name="cells_boundaries_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load cells boundaries?"/> <param name="cells_table_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load cells table?"/> <param name="mosaic_images_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load mosaic images?"/> </when> <when value="visium"> <param name="dataset_id" type="text" value="Galaxy" label="Dataset identifier to name the constructed SpatialData elements"> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> <add value="_" /> </valid> </sanitizer> <validator type="regex">[0-9a-zA-Z_]+</validator> </param> <param name="feature_bc_matrix" type="data" format="h5" label="feature BC matrix (Counts file)"/> <param name="matrix_bool" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Is the matrix input, raw?" help="If the matrix input is raw, set this to true." /> <param name="scalefactors_json" type="data" format="json" label="Scale factors file"/> <param name="fullres_image_file" type="data" format="tiff" label="Full resolution image"/> <param name="tissue_hires_image" type="data" format="png" label="Tissue high resolution image"/> <param name="tissue_lowres_image" type="data" format="png" label="Tissue low resolution image"/> <param name="tissue_positions_list" type="data" format="csv" label="Tissue positions file"/> </when> <when value="visium_hd"> <param name="dataset_id" type="text" value="Galaxy" label="Dataset identifier" help="Name for the constructed SpatialData elements"> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> <add value="_" /> </valid> </sanitizer> <validator type="regex">[0-9a-zA-Z_]+</validator> </param> <param name="matrix_bool" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Is the matrix input, raw?" help="If the matrix input is raw, set this to true."/> <param name="feature_slice" type="data" format="h5" label="Feature slice file"/> <conditional name="include_binned_condi"> <param name="include_binned" type="select" label="Include binned data?"> <option value="yes">Yes</option> <option value="no">No</option> </param> <when value="no"/> <when value="yes"> <section name="bin008" title="Binned outputs 008"> <param name="feature_bc_matrix_008" type="data" format="h5" optional="true" label="Feature BC matrix of bin 008"/> <param name="tissue_positions_008" type="data" format="parquet" optional="true" label="Tissue positions of bin 008"/> <param name="scalefactors_json_008" type="data" format="json" optional="true" label="Scale factors of bin 008"/> </section> <section name="bin016" title="Binned outputs 016"> <param name="feature_bc_matrix_016" type="data" format="h5" optional="true" label="Feature BC matrix of bin 016"/> <param name="tissue_positions_016" type="data" format="parquet" optional="true" label="Tissue positions of bin 016"/> <param name="scalefactors_json_016" type="data" format="json" optional="true" label="Scale factors of bin 016"/> </section> <conditional name="include_nucleus_seg_condi"> <param name="include_nucleus_seg" type="select" label="Include nucleus segmentation?"> <option value="yes">Yes</option> <option value="no">No</option> </param> <when value="no"> <section name="bin002" title="Binned outputs 002"> <param name="feature_bc_matrix_002" type="data" format="h5" optional="true" label="Feature BC matrix of bin 002"/> <param name="tissue_positions_002" type="data" format="parquet" optional="true" label="Tissue positions of bin 002"/> <param name="scalefactors_json_002" type="data" format="json" optional="true" label="Scale factors of bin 002"/> </section> </when> <when value="yes"> <section name="bin002" title="Binned outputs 002"> <param name="feature_bc_matrix_002" type="data" format="h5" optional="false" label="Feature BC matrix of bin 002"/> <param name="tissue_positions_002" type="data" format="parquet" optional="false" label="Tissue positions of bin 002"/> <param name="scalefactors_json_002" type="data" format="json" optional="false" label="Scale factors of bin 002"/> </section> <param name="nucleus_segmentation" type="data" format="geojson" optional="false" label="Nucleus segmentation GeoJSON"/> <param name="barcode_mappings" type="data" format="parquet" optional="false" label="Barcode mappings"/> </when> </conditional> </when> </conditional> <conditional name="segmentation_conditional"> <param name="enable_segmentation" type="select" label="Include segmentation data?"> <option value="yes">Yes</option> <option value="no">No</option> </param> <when value="no"/> <when value="yes"> <param name="feature_bc_matrix_seg" type="data" format="h5" optional="false" label="Feature BC matrix of cell segmentation"/> <param name="cell_segmentation" type="data" format="geojson" optional="false" label="Cell segmentation GeoJSON"/> <param name="scalefactors_json_seg" type="data" format="json" optional="false" label="Scale factors of cell segmentation"/> </when> </conditional> <section name="images" title="Images"> <param name="microscope_image" type="data" format="png,tiff,jpg" optional="true" label="Microscope image" help="Full-resolution microscope image (png/tiff/jpg)"/> <param name="tissue_hires" type="data" format="png" optional="true" label="Tissue high-res image" help="tissue_hires_image.png"/> <param name="tissue_lowres" type="data" format="png" optional="true" label="Tissue low-res image" help="tissue_lowres_image.png"/> <conditional name="cytassist_image_condi"> <param name="include_cytassist" type="select" label="Include CytAssist image?"> <option value="yes">Yes</option> <option value="no">No</option> </param> <when value="no"/> <when value="yes"> <param name="cytassist_image" type="data" format="tiff" optional="false" label="CytAssist image"/> </when> </conditional> </section> <param name="bins_as_squares_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load bins as squares?" help="If True, bins are represented as squares; if False, as circles"/> <param name="annotate_table_by_labels_bool" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Annotate table by labels?" help="Annotate the AnnData table with cell/nucleus labels"/> <param name="var_names_make_unique_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Make variable names unique?" help="If True, call .var_names_make_unique() on each AnnData table"/> </when> <when value="xenium"> <param name="cell_feature_matrix" type="data" format="h5" label="Cell feature matrix"/> <param name="cells" type="data" format="parquet" label="Cells metadata"/> <param name="cells_zarr" type="data" format="zarr.zip" label="Cells zarr archive"/> <param name="experiment_xenium" type="data" format="json" label="Experiment xenium file containing specifications"/> <param name="morphology_focus" type="data" format="ome.tiff" multiple="true" label="Morphology focus images" help="Both MIP and Focus"/> <param name="cell_boundaries" type="data" optional="true" format="parquet" label="Polygons of cell boundaries"/> <param name="nucleus_boundaries" type="data" optional="true" format="parquet" label="Polygons of nucleus boundaries"/> <param name="transcripts" type="data" optional="true" format="parquet" label="Transcripts"/> <param name="cells_as_circles_bool" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Represent cells as circles?" help="The center and the radius of each circle is computed from the corresponding labels cell"/> <param name="cells_labels_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load cells labels?"/> <param name="nucleus_labels_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load nucleus labels?"/> <param name="morphology_mip_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load morphology MIP?"/> <param name="morphology_focus_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load morphology focus?"/> <param name="cells_table_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load cells annotation from AnnData?"/> <param name="gex_only_bool" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Load gene expression only?"/> <conditional name="add_hne_condi"> <param name="add_hne" type="select" label="Add H&E image?"> <option value="yes_accurate">Yes, with accurate alignment</option> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <when value="no"/> <when value="yes_accurate"> <param name="hne_image" type="data" format="ome.tiff" label="H&E image"/> <param name="image_alignment" type="data" format="csv" label="Image alignment file"/> </when> <when value="yes"> <param name="hne_image" type="data" format="ome.tiff" label="H&E image"/> </when> </conditional> <conditional name="add_if_condi"> <param name="add_if" type="select" label="Add IF image?"> <option value="yes_accurate">Yes, with accurate alignment</option> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <when value="no"/> <when value="yes_accurate"> <param name="if_image" type="data" format="ome.tiff" label="IF image"/> <param name="image_alignment" type="data" format="csv" label="Image alignment file"/> </when> <when value="yes"> <param name="if_image" type="data" format="ome.tiff" label="IF image"/> </when> </conditional> </when> </conditional> </inputs> <outputs> <data name="spatialdata_output" format="spatialdata.zip" from_work_dir="spatialdata.spatialdata.zip" label="${tool.name} on ${on_string}: spatialdata"/> </outputs> <tests> <!-- test 1: io MERSCOPE full --> <test> <conditional name="method_condi"> <param name="method" value="merscope"/> <param name="slide_name" value="Test_MERSCOPE"/> <param name="region_name" value="sample_region"/> <param name="mosaic_images" location="https://zenodo.org/records/18746346/files/mosaic_Cellbound1_z2.tif,https://zenodo.org/records/18746346/files/mosaic_Cellbound1_z3.tif,https://zenodo.org/records/18746346/files/mosaic_Cellbound2_z2.tif,https://zenodo.org/records/18746346/files/mosaic_Cellbound2_z3.tif,https://zenodo.org/records/18746346/files/mosaic_Cellbound3_z2.tif,https://zenodo.org/records/18746346/files/mosaic_Cellbound3_z3.tif,https://zenodo.org/records/18746346/files/mosaic_DAPI_z2.tif,https://zenodo.org/records/18746346/files/mosaic_DAPI_z3.tif,https://zenodo.org/records/18746346/files/mosaic_PolyT_z2.tif,https://zenodo.org/records/18746346/files/mosaic_PolyT_z3.tif"/> <param name="z_layers" value="3"/> <param name="input_micron_to_mosaic" location="https://zenodo.org/records/18746346/files/merscope_micron_to_mosaic_pixel_transform.csv"/> <param name="cell_by_gene" location="https://zenodo.org/records/18746346/files/merscope_cell_by_gene.csv"/> <param name="cell_meta" location="https://zenodo.org/records/18746346/files/merscope_cell_metadata.csv"/> <param name="cells_boundaries" location="https://zenodo.org/records/18746346/files/merscope_cellpose2_micron_space.parquet"/> <param name="transcripts" location="https://zenodo.org/records/18746346/files/merscope_detected_transcripts.csv"/> </conditional> <assert_stdout> <has_text text="z_layers=[3]"/> <has_text text="'Test_MERSCOPE_sample_region_polygons': GeoDataFrame shape: (928, 9)"/> <has_text text="'table': AnnData (928, 130)"/> </assert_stdout> <output name="spatialdata_output"> <assert_contents> <has_archive_member path="spatialdata/zarr.json"> <has_text text=""zarr_format": 3"/> <has_text text=""label": "DAPI""/> </has_archive_member> </assert_contents> </output> </test> <!-- test 2: io COSMX full --> <test> <conditional name="method_condi"> <param name="method" value="cosmx"/> <param name="CellComposite" location="https://zenodo.org/records/18746346/files/cosmx_CellComposite_F001.jpg"/> <param name="CellLabels" location="https://zenodo.org/records/18746346/files/cosmx_CellLabels_F001.tif"/> <param name="exprMat_file" location="https://zenodo.org/records/18746346/files/cosmx_dummy_exprMat_file.csv"/> <param name="fov_positions_file" location="https://zenodo.org/records/18746346/files/cosmx_dummy_fov_positions_file.csv"/> <param name="metadata_file" location="https://zenodo.org/records/18746346/files/cosmx_dummy_metadata_file.csv"/> <param name="tx_file" location="https://zenodo.org/records/18746346/files/cosmx_dummy_tx_file.csv"/> <param name="dataset_id" value="cosmx_dummy"/> <param name="transcripts_bool" value="True"/> </conditional> <output name="spatialdata_output"> <assert_contents> <has_archive_member path="spatialdata/zarr.json"> <has_text text=""zarr_format": 3"/> <has_text text="images/1_image"/> </has_archive_member> </assert_contents> </output> </test> <!-- test 3: io dbit full--> <test> <conditional name="method_condi"> <param name="method" value="dbit"/> <param name="barcode_positions" location="https://zenodo.org/records/18746346/files/dbit_barcode_positions.txt"/> <param name="counts" location="https://zenodo.org/records/18746346/files/dbit_counts.h5ad"/> <param name="tissue_lowres" location="https://zenodo.org/records/18746346/files/dbit_tissue_lowres.png"/> </conditional> <assert_stdout> <has_text text="'Galaxy': GeoDataFrame shape: (500, 1) (2D shapes)"/> <has_text text="'table': AnnData (500, 1000)"/> </assert_stdout> <output name="spatialdata_output"> <assert_contents> <has_archive_member path="spatialdata/zarr.json"> <has_text text=""zarr_format": 3"/> <has_text text="images/Galaxy_image"/> </has_archive_member> </assert_contents> </output> </test> <!-- test 4: io macsima full--> <test> <conditional name="method_condi"> <param name="method" value="macsima"/> <param name="tiff_files" location="https://zenodo.org/records/18746346/files/macima_C-001_S-000_S_APC_R-01_W-D01_ROI-01_A-CD3_C-REA1151.tif,https://zenodo.org/records/18746346/files/macima_C-002_S-000_S_PE_R-01_W-D01_ROI-01_A-CD279_C-REA1165.tif,https://zenodo.org/records/18746346/files/macima_C-015_S-000_B_DAPI_R-01_W-D01_ROI-01_A-DAPI.tif,https://zenodo.org/records/18746346/files/macima_C-001_S-000_S_DAPI_R-01_W-D01_ROI-01_A-DAPI.tif,https://zenodo.org/records/18746346/files/macima_C-004_S-000_S_FITC_R-01_W-D01_ROI-01_A-CD66b_C-REA306.tif"/> </conditional> <assert_stdout> <has_text text="'input_image': DataTree"/> <has_text text="'input_table': AnnData (0, 5)"/> </assert_stdout> <output name="spatialdata_output"> <assert_contents> <has_archive_member path="spatialdata/zarr.json"> <has_text text=""zarr_format": 3"/> <has_text text="images/input_image"/> </has_archive_member> </assert_contents> </output> </test> <!-- test 5: io VISIUM full --> <test> <conditional name="method_condi"> <param name="method" value="visium"/> <param name="dataset_id" value="Test_Visium"/> <param name="feature_bc_matrix" location="https://zenodo.org/records/18746346/files/visium_CytAssist_FFPE_Protein_Expression_Human_Tonsil_filtered_feature_bc_matrix.h5"/> <param name="matrix_bool" value="false"/> <param name="scalefactors_json" location="https://zenodo.org/records/18746346/files/visium_scalefactors_json.json"/> <param name="fullres_image_file" location="https://zenodo.org/records/18746346/files/visium_CytAssist_FFPE_Protein_Expression_Human_Tonsil_image.tif"/> <param name="tissue_hires_image" location="https://zenodo.org/records/18746346/files/visium_tissue_hires_image.png"/> <param name="tissue_lowres_image" location="https://zenodo.org/records/18746346/files/visium_tissue_lowres_image.png"/> <param name="tissue_positions_list" location="https://zenodo.org/records/18746346/files/visium_tissue_positions.csv"/> </conditional> <assert_stdout> <has_text text="'Test_Visium': GeoDataFrame shape: (4194, 2)"/> <has_text text="'table': AnnData (4194, 18085)"/> </assert_stdout> <output name="spatialdata_output"> <assert_contents> <has_archive_member path="spatialdata/zarr.json"> <has_text text=""zarr_format": 3"/> <has_text text="images/Test_Visium_full_image"/> </has_archive_member> </assert_contents> </output> </test> <!-- test 6: io Visium HD full --> <test> <conditional name="method_condi"> <param name="method" value="visium_hd"/> <param name="dataset_id" value="Test_VisiumHD"/> <param name="matrix_bool" value="false"/> <param name="feature_slice" location="https://zenodo.org/records/18746346/files/visiumhd_feature_slice.h5"/> <conditional name="include_binned_condi"> <param name="include_binned" value="yes"/> <section name="bin008"> <param name="feature_bc_matrix_008" location="https://zenodo.org/records/18746346/files/visiumhd_filtered_feature_bc_matrix_008.h5"/> <param name="tissue_positions_008" location="https://zenodo.org/records/18746346/files/visiumhd_tissue_positions_008.parquet"/> <param name="scalefactors_json_008" location="https://zenodo.org/records/18746346/files/visiumhd_scalefactors_json_008.json"/> </section> <section name="bin016"> <param name="feature_bc_matrix_016" location="https://zenodo.org/records/18746346/files/visiumhd_filtered_feature_bc_matrix_016.h5"/> <param name="tissue_positions_016" location="https://zenodo.org/records/18746346/files/visiumhd_tissue_positions_016.parquet"/> <param name="scalefactors_json_016" location="https://zenodo.org/records/18746346/files/visiumhd_scalefactors_json_016.json"/> </section> <conditional name="include_nucleus_seg_condi"> <param name="include_nucleus_seg" value="yes"/> <section name="bin002"> <param name="feature_bc_matrix_002" location="https://zenodo.org/records/18746346/files/visiumhd_filtered_feature_bc_matrix_002.h5"/> <param name="tissue_positions_002" location="https://zenodo.org/records/18746346/files/visiumhd_tissue_positions_002.parquet"/> <param name="scalefactors_json_002" location="https://zenodo.org/records/18746346/files/visiumhd_scalefactors_json_002.json"/> </section> <param name="nucleus_segmentation" location="https://zenodo.org/records/18746346/files/visiumhd_nucleus_segmentations.geojson"/> <param name="barcode_mappings" location="https://zenodo.org/records/18746346/files/visiumhd_barcode_mappings.parquet"/> </conditional> </conditional> <conditional name="segmentation_conditional"> <param name="enable_segmentation" value="yes"/> <param name="feature_bc_matrix_seg" location="https://zenodo.org/records/18746346/files/visiumhd_filtered_feature_cell_matrix_seg.h5"/> <param name="cell_segmentation" location="https://zenodo.org/records/18746346/files/visiumhd_cell_segmentations.geojson"/> <param name="scalefactors_json_seg" location="https://zenodo.org/records/18746346/files/visiumhd_scalefactors_json_seg.json"/> </conditional> <section name="images"> <param name="tissue_hires" location="https://zenodo.org/records/18746346/files/visiumhd_tissue_hires_image.png"/> <param name="tissue_lowres" location="https://zenodo.org/records/18746346/files/visiumhd_tissue_lowres_image.png"/> <conditional name="cytassist_image_condi"> <param name="include_cytassist" value="yes"/> <param name="cytassist_image" location="https://zenodo.org/records/18746346/files/visiumhd_cytassist_image.tiff"/> </conditional> </section> <param name="bins_as_squares_bool" value="true"/> <param name="annotate_table_by_labels_bool" value="false"/> <param name="var_names_make_unique_bool" value="true"/> </conditional> <assert_stdout> <has_text text="'Test_VisiumHD"/> <has_text text="Tables"/> <has_text text="'cell_segmentations': AnnData"/> </assert_stdout> <output name="spatialdata_output"> <assert_contents> <has_archive_member path="spatialdata/zarr.json"> <has_text text=""zarr_format": 3"/> </has_archive_member> </assert_contents> </output> </test> <!-- test 7: io XENIUM full --> <test> <conditional name="method_condi"> <param name="method" value="xenium"/> <param name="cell_feature_matrix" location="https://zenodo.org/records/18746346/files/xenium_cell_feature_matrix.h5"/> <param name="cells" location="https://zenodo.org/records/18746346/files/xenium_cells.parquet"/> <param name="cells_zarr" location="https://zenodo.org/records/18746346/files/xenium_cells.zarr.zip"/> <param name="experiment_xenium" location="https://zenodo.org/records/18746346/files/xenium_experiment.xenium"/> <param name="morphology_focus" location="https://zenodo.org/records/18746346/files/ch0000_dapi.ome.tif,https://zenodo.org/records/18746346/files/ch0006_yellow_background.ome.tif,https://zenodo.org/records/18746346/files/ch0001_atp1a1_cd45_e-cadherin.ome.tif,https://zenodo.org/records/18746346/files/ch0007_red_background.ome.tif,https://zenodo.org/records/18746346/files/ch0002_18s.ome.tif,https://zenodo.org/records/18746346/files/ch0008_pd-1.ome.tif,https://zenodo.org/records/18746346/files/ch0003_alphasma_vimentin.ome.tif,https://zenodo.org/records/18746346/files/ch0009_vista.ome.tif,https://zenodo.org/records/18746346/files/ch0004_blue_background.ome.tif,https://zenodo.org/records/18746346/files/ch0010_pd-l1.ome.tif,https://zenodo.org/records/18746346/files/ch0005_green_background.ome.tif,https://zenodo.org/records/18746346/files/ch0011_lag-3.ome.tif"/> <param name="cell_boundaries" location="https://zenodo.org/records/18746346/files/xenium_cell_boundaries.parquet"/> <param name="nucleus_boundaries" location="https://zenodo.org/records/18746346/files/xenium_nucleus_boundaries.parquet"/> <param name="transcripts" location="https://zenodo.org/records/18746346/files/xenium_transcripts.parquet"/> <conditional name="add_hne_condi"> <param name="add_hne" value="yes"/> <param name="hne_image" location="https://zenodo.org/records/18746346/files/xenium_he_image.ome.tif"/> </conditional> </conditional> <assert_stdout> <has_text text="'cell_labels': DataTree"/> <has_text text="'table': AnnData (358, 405)"/> </assert_stdout> <output name="spatialdata_output"> <assert_contents> <has_archive_member path="spatialdata/zarr.json"> <has_text text=""zarr_format": 3"/> <has_text text="images/morphology_focus"/> </has_archive_member> </assert_contents> </output> </test> <!-- test 8: io XENIUM full accurate--> <test> <conditional name="method_condi"> <param name="method" value="xenium"/> <param name="cell_feature_matrix" location="https://zenodo.org/records/18746346/files/xenium_cell_feature_matrix.h5"/> <param name="cells" location="https://zenodo.org/records/18746346/files/xenium_cells.parquet"/> <param name="cells_zarr" location="https://zenodo.org/records/18746346/files/xenium_cells.zarr.zip"/> <param name="experiment_xenium" location="https://zenodo.org/records/18746346/files/xenium_experiment.xenium"/> <param name="morphology_focus" location="https://zenodo.org/records/18746346/files/ch0000_dapi.ome.tif,https://zenodo.org/records/18746346/files/ch0006_yellow_background.ome.tif,https://zenodo.org/records/18746346/files/ch0001_atp1a1_cd45_e-cadherin.ome.tif,https://zenodo.org/records/18746346/files/ch0007_red_background.ome.tif,https://zenodo.org/records/18746346/files/ch0002_18s.ome.tif,https://zenodo.org/records/18746346/files/ch0008_pd-1.ome.tif,https://zenodo.org/records/18746346/files/ch0003_alphasma_vimentin.ome.tif,https://zenodo.org/records/18746346/files/ch0009_vista.ome.tif,https://zenodo.org/records/18746346/files/ch0004_blue_background.ome.tif,https://zenodo.org/records/18746346/files/ch0010_pd-l1.ome.tif,https://zenodo.org/records/18746346/files/ch0005_green_background.ome.tif,https://zenodo.org/records/18746346/files/ch0011_lag-3.ome.tif"/> <param name="cell_boundaries" location="https://zenodo.org/records/18746346/files/xenium_cell_boundaries.parquet"/> <param name="nucleus_boundaries" location="https://zenodo.org/records/18746346/files/xenium_nucleus_boundaries.parquet"/> <param name="transcripts" location="https://zenodo.org/records/18746346/files/xenium_transcripts.parquet"/> <conditional name="add_hne_condi"> <param name="add_hne" value="yes_accurate"/> <param name="hne_image" location="https://zenodo.org/records/18746346/files/xenium_he_image.ome.tif"/> <param name="image_alignment" location="https://zenodo.org/records/18746346/files/xenium_he_image_alignment.csv"/> </conditional> </conditional> <assert_stdout> <has_text text="'cell_labels': DataTree"/> <has_text text="'table': AnnData (358, 405)"/> <has_text text="xenium_aligned_image"/> </assert_stdout> <output name="spatialdata_output"> <assert_contents> <has_archive_member path="spatialdata/zarr.json"> <has_text text=""zarr_format": 3"/> <has_text text="images/morphology_focus"/> </has_archive_member> </assert_contents> </output> </test> </tests> <help><![CDATA[ **What it does** This tool loads common spatial omics data formats into the SpatialData framework, a unified data structure for spatial omics data. It supports multiple spatial transcriptomics and proteomics technologies, converting their native output formats into a standardized SpatialData object stored as a Zarr archive. ----- **Supported Technologies** - **10x Genomics Visium**: Standard Visium spatial gene expression data - **10x Genomics Visium HD**: High-definition Visium with multiple bin sizes and segmentation data - **10x Genomics Xenium**: In situ spatial transcriptomics with subcellular resolution - **CosMx SMI (Nanostring)**: Spatial molecular imaging platform - **MERSCOPE (Vizgen)**: Multiplexed error-robust fluorescence in situ hybridization - **MACSima (Miltenyi)**: Multiplexed antibody-based imaging for cyclic staining - **DBiT-seq**: Deterministic Barcoding in Tissue for spatial omics ----- **Output** The tool produces a SpatialData object saved as a compressed Zarr archive (.spatialdata.zip). This archive contains: - **Images**: H&E, staining images - **Labels**: Pixel-level segmentation - **Shapes**: Cell/nucleus boundaries, subcellular structures, anatomical annotations, regions of interest (ROIs) - **Points**: Transcripts locations with gene information, landmarks points - **Tables**: AnnData objects with gene expression matrices and metadata The SpatialData format enables downstream analysis with tools like squidpy, spatialdata-plot, and napari for interactive visualization. ----- **More Information** - `SpatialData documentation <https://spatialdata.scverse.org/projects/io/en/stable/>`__ ]]></help> <expand macro="citations" /> </tool>