API of Open-ST tools¶
Here we show the description of all commands available in the openst tools, which can be run as:
barcode_preprocessing¶
Convert spatial barcode raw data into tabular files with barcodes and spatial coordinates.
Usage:
openst barcode_preprocessing [-h] --fastq-in FASTQ_IN --tilecoords-out TILECOORDS_OUT --out-suffix OUT_SUFFIX [--out-prefix OUT_PREFIX] [--crop-seq CROP_SEQ] [--rev-comp] [--single-tile] [--unsorted]
options:
-h, --help show this help message and exit
--fastq-in FASTQ_IN Path to the fastq file
--tilecoords-out TILECOORDS_OUT
Directory where output files will be written to
--out-suffix OUT_SUFFIX
Suffix added to the name of the output files (i.e., extension)
--out-prefix OUT_PREFIX
(Optional) Prefix added to the name of the output files. Default: ""
--crop-seq CROP_SEQ (Optional) A 'python-style' slice, used to crop input sequences. Default: ":"
--rev-comp (Optional) Apply reverse complementary after sequence cropping
--single-tile (Optional) set if it is guarranteed that the input .fastq(.gz) file contains only a tile
--unsorted (Optional) set when file is unsorted respect to tiles; might be slower
image_stitch¶
Stitch image fields of view into a single image. Currently, it only supports --microscope keyence, for the
default microscopy setup used in our paper.
Usage:
openst image_stitch [-h] --image-indir IMAGE_INDIR --image-out IMAGE_OUT --imagej-bin IMAGEJ_BIN --microscope {keyence} [--no-run] [--rerun] [--metadata METADATA] [--join-zstack-regex JOIN_ZSTACK_REGEX]
options:
-h, --help show this help message and exit
--image-indir IMAGE_INDIR
path to collection of images
--image-out IMAGE_OUT
path where to save the image (must be a filename)
--imagej-bin IMAGEJ_BIN
path to the ImageJ/Fiji executable. Must have the Grid Collection plugin available!
--microscope {keyence}
microscope model or imaging strategy that was used for imaging
--no-run If set, do not run ImageJ, but return the command line
--rerun If set, runs stitching even when the output file exists
--metadata METADATA Path where the metadata will be stored. If not specified, metadata is not saved. Default: ""
--join-zstack-regex JOIN_ZSTACK_REGEX
When non empty, this specifies how to find the Z location from the individual filename and will create a z-stack from single images. Example regex: 'Image_([0-9]*)_Z([0-9]*)_CH1.tif'. Default: ""
image_preprocess¶
Restoration of imaging data with CUT model, as in Open-ST paper.
Usage:
openst image_preprocess [-h] [--h5-in H5_IN] [--image-in IMAGE_IN] [--image-out IMAGE_OUT] [--tile-size-px TILE_SIZE_PX] [--model MODEL] [--device {cpu,cuda}] [--num-workers NUM_WORKERS]
options:
-h, --help show this help message and exit
--h5-in H5_IN If set, image is loaded from the Open-ST h5 object (key in --image-in), and retored image is saved there (to the key --image-out). Default: ""
--image-in IMAGE_IN Key or path to the input image. Default: ""
--image-out IMAGE_OUT
Key or path where the restored image will be written into. Default: ""
--tile-size-px TILE_SIZE_PX
The input image is split into squared tiles of side `--tile-size-px`, for inference.Larger values avoid boundary effects, but require more memory. Default: 512
--model MODEL CUT model used for image restoration. Default: "HE_CUT_rajewsky"
--device {cpu,cuda} Device used to run CUT restoration model. Can be ['cpu', 'cuda']. Default: "cpu"
--num-workers NUM_WORKERS
Number of CPU workers for parallel processing. Default: -1
spatial_stitch¶
Stitch Open-ST h5 tile objects into a single Open-ST h5 object.
Usage:
openst spatial_stitch [-h] --tiles TILES [TILES ...] --tile-coordinates TILE_COORDINATES [--tile-id TILE_ID [TILE_ID ...]] [--tile-id-regex TILE_ID_REGEX] --h5-out H5_OUT [--tile-id-key TILE_ID_KEY]
[--merge-output {same,unique,first,only}] [--join-output {inner,outer}] [--no-reset-index] [--no-transform] [--metadata METADATA]
options:
-h, --help show this help message and exit
--tiles TILES [TILES ...]
Path to h5 file, one per tile - separated by space
--tile-coordinates TILE_COORDINATES
Path to the coordinate system file
--tile-id TILE_ID [TILE_ID ...]
(Mandatory if --tile-id-regex is not specified) Per tile file specified in --tiles, each entry in --tile-id maps a tile file to the tile IDs under the first column of the --tile-
coordinates file.
--tile-id-regex TILE_ID_REGEX
(Mandatory if --tile-id is not specified) "Regex to find tile id in file names, instead of specifying a list in --tile-id. Default: "(L[1-4][a-b]_tile_[1-2][0-7][0-9][0-9])"
--h5-out H5_OUT Where the stitched spatial object will be written to
--tile-id-key TILE_ID_KEY
Key of the h5 file (under /obs) where tile IDs are stored. If != 'tile_id', a new categorical column of this name will be generated for consistency. Default: "tile_id"
--merge-output {same,unique,first,only}
how to merge tiles, can be "same", "unique", "first", "only". Default: "same"
--join-output {inner,outer}
how to join tiles, can be "inner", "outer". Default: "outer"
--no-reset-index If set, do not reset the obs_name index of the combined spatial object as 'obs_name:<tile_id_key>'; keep original 'obs_name'.
--no-transform If set, spatial coordinates are not transformed - just combine tiles into a single spatial object
--metadata METADATA (Optional) Path where the metadata will be stored. If not specified, metadata is not saved. Default: ""
merge_modalities¶
Merges spatial locations (as points) and images of Open-ST data into a single h5 object.
Usage
openst merge_modalities [-h] --h5-in H5_IN --image-in IMAGE_IN [--image-key IMAGE_KEY]
options:
-h, --help show this help message and exit
--h5-in H5_IN Input Open-ST h5 object
--image-in IMAGE_IN Image that will be loaded and written into the Open-ST h5 object
--image-key IMAGE_KEY
Key in the Open-ST h5 object where the image will be saved. Default: "uns/spatial/staining_image"
pairwise_aligner¶
Automatic pairwise alignment of transcript locations to imaging data.
Usage:
openst pairwise_aligner [-h] --h5-in H5_IN [--image-in IMAGE_IN] [--metadata METADATA] [--only-coarse] [--rescale-factor-coarse RESCALE_FACTOR_COARSE] [--threshold-counts-coarse THRESHOLD_COUNTS_COARSE]
[--pseudoimage-size-coarse PSEUDOIMAGE_SIZE_COARSE] [--ransac-coarse-min-samples RANSAC_COARSE_MIN_SAMPLES] [--ransac-coarse-residual-threshold RANSAC_COARSE_RESIDUAL_THRESHOLD]
[--ransac-coarse-max-trials RANSAC_COARSE_MAX_TRIALS] [--genes-coarse GENES_COARSE [GENES_COARSE ...]] [--rescale-factor-fine RESCALE_FACTOR_FINE]
[--tissue-masking-gaussian-sigma TISSUE_MASKING_GAUSSIAN_SIGMA] [--fine-registration-gaussian-sigma FINE_REGISTRATION_GAUSSIAN_SIGMA]
[--threshold-counts-fine THRESHOLD_COUNTS_FINE] [--pseudoimage-size-fine PSEUDOIMAGE_SIZE_FINE] [--ransac-fine-min-samples RANSAC_FINE_MIN_SAMPLES]
[--ransac-fine-residual-threshold RANSAC_FINE_RESIDUAL_THRESHOLD] [--ransac-fine-max-trials RANSAC_FINE_MAX_TRIALS] [--fine-min-matches FINE_MIN_MATCHES]
[--genes-fine GENES_FINE [GENES_FINE ...]] [--mask-tissue] [--keep-black-background] [--feature-matcher {LoFTR,SIFT,KeyNet}] [--fiducial-model FIDUCIAL_MODEL]
[--num-workers NUM_WORKERS] [--device {cpu,cuda}]
options:
-h, --help show this help message and exit
Data (required):
--h5-in H5_IN Path to the merged Open-ST h5 object containing spatial coordinates and images
Data (optional):
--image-in IMAGE_IN Key to the image used as the 'destination' during pairwise alignment. Default: "uns/spatial/staining_image"
--metadata METADATA Path where the metadata will be stored. If not specified, metadata is not saved. Default: ""
Coarse registration parameters:
--only-coarse If selected, only the coarse alignment stage will run
--rescale-factor-coarse RESCALE_FACTOR_COARSE
Rescaling factor for the input image (1:factor), used during coarse pairwise alignment. Default: 20
--threshold-counts-coarse THRESHOLD_COUNTS_COARSE
Only spatial coordinates with counts larger than this number will be kept for pseudoimage rendering during coarse alignment. Default: 1
--pseudoimage-size-coarse PSEUDOIMAGE_SIZE_COARSE
Size (in pixels) of the pseudoimage during coarse alignment. Default: 500
--ransac-coarse-min-samples RANSAC_COARSE_MIN_SAMPLES
'min_samples' parameter of RANSAC, during coarse registration. Default: 3
--ransac-coarse-residual-threshold RANSAC_COARSE_RESIDUAL_THRESHOLD
'residual_threshold' parameter of RANSAC, during coarse registration. Default: 2
--ransac-coarse-max-trials RANSAC_COARSE_MAX_TRIALS
Times RANSAC will run (x1000 iterations) during coarse registration. Default: 2
--genes-coarse GENES_COARSE [GENES_COARSE ...]
Genes used for plotting the pseudoimage during the coarse alignment phase. Default: None
Fine registration parameters:
--rescale-factor-fine RESCALE_FACTOR_FINE
Rescaling factor for the input image (1:factor), used during fine pairwise alignment. Default: 10
--tissue-masking-gaussian-sigma TISSUE_MASKING_GAUSSIAN_SIGMA
The gaussian blur sigma used during the isolation of the tissue on the HE (preprocessing). Default: 5
--fine-registration-gaussian-sigma FINE_REGISTRATION_GAUSSIAN_SIGMA
Gaussian blur used on all modalities during fine registration. Default: 2
--threshold-counts-fine THRESHOLD_COUNTS_FINE
Only spatial coordinates with counts larger than this number will be kept for pseudoimage rendering during fine alignment. Default: 0
--pseudoimage-size-fine PSEUDOIMAGE_SIZE_FINE
Size (in pixels) of the pseudoimage during fine alignment. Default: 2000
--ransac-fine-min-samples RANSAC_FINE_MIN_SAMPLES
'min_samples' parameter of RANSAC, during fine registration. Default: 3
--ransac-fine-residual-threshold RANSAC_FINE_RESIDUAL_THRESHOLD
'residual_threshold' parameter of RANSAC, during fine registration. Default: 2
--ransac-fine-max-trials RANSAC_FINE_MAX_TRIALS
Times RANSAC will run (x1000 iterations) during fine registration. Default: 2
--fine-min-matches FINE_MIN_MATCHES
Minimum number of matching keypoints between modalities during fine alignment. Default: 50
--genes-fine GENES_FINE [GENES_FINE ...]
Genes used for plotting the pseudoimage during the fine alignment phase. Default: None
Image preprocessing parameters:
--mask-tissue Tissue (imaging modality) is masked from the background for the feature detection
--keep-black-background
Whether to set the background of the imaging modalities to white, after tissue masking
Feature model parameters:
--feature-matcher {LoFTR,SIFT,KeyNet}
Feature matching algorithm. Default: "LoFTR"
--fiducial-model FIDUCIAL_MODEL
Path to a object detection model (YOLO) to detect fiducial markers. Default: ""
Computational parameters:
--num-workers NUM_WORKERS
Number of CPU workers for parallel processing. Default: 1
--device {cpu,cuda} Device used to run feature matching model. Can be ['cpu', 'cuda']. Default: "cpu"
apply_transform¶
Apply a precomputed transformation matrix to the specified coordinates of an Open-ST h5 object
Usage:
openst apply_transform [-h] --keypoints-in KEYPOINTS_IN --h5-in H5_IN [--per-tile] [--spatial-key-in SPATIAL_KEY_IN] [--spatial-key-out SPATIAL_KEY_OUT]
options:
-h, --help show this help message and exit
--keypoints-in KEYPOINTS_IN
Path to the json file containing keypoints.
--h5-in H5_IN Path to the input h5ad file containing spatial coordinates
--per-tile (Optional) If set, transformations are applied per tile, from their keypoints. Otherwise, a single transform is computed for all tiles.
--spatial-key-in SPATIAL_KEY_IN
Key of the Open-ST h5 object where the input spatial coordinates are read from. Default: "obsm/spatial_pairwise_aligned_coarse"
--spatial-key-out SPATIAL_KEY_OUT
Key of the Open-ST h5 object where the transformed spatial coordinates are written into. Default: "obsm/spatial_pairwise_aligned_fine"
manual_pairwise_aligner¶
GUI for manual alignment of Open-ST data
openst manual_pairwise_aligner [-h] [--h5-in H5_IN] [--spatial-key SPATIAL_KEY] [--image-key IMAGE_KEY]
options:
-h, --help show this help message and exit
--h5-in H5_IN Path to the input h5ad file containing spatial coordinates. Default: ""
--spatial-key SPATIAL_KEY
Path in the h5ad file to the spatial coordinates. Default: ""
--image-key IMAGE_KEY
Path in the h5ad file to the image. Default: ""
segment¶
Image (or pseudoimage)-based segmentation with cellpose and (optional) radial extension
Usage:
openst segment [-h] [--image-in IMAGE_IN] [--h5-in H5_IN] --mask-out MASK_OUT [--rna-segment] [--model MODEL] [--flow-threshold FLOW_THRESHOLD] [--cellprob-threshold CELLPROB_THRESHOLD]
[--diameter DIAMETER] [--chunk-size CHUNK_SIZE] [--chunked] [--max-image-pixels MAX_IMAGE_PIXELS] [--device {cpu,cuda}] [--dilate-px DILATE_PX] [--outline-px OUTLINE_PX] [--mask-tissue]
[--tissue-masking-gaussian-sigma TISSUE_MASKING_GAUSSIAN_SIGMA] [--keep-black-background] [--rna-segment-spatial-coord-key RNA_SEGMENT_SPATIAL_COORD_KEY]
[--rna-segment-input-resolution RNA_SEGMENT_INPUT_RESOLUTION] [--rna-segment-render-scale RNA_SEGMENT_RENDER_SCALE] [--rna-segment-render-sigma RNA_SEGMENT_RENDER_SIGMA]
[--rna-segment-output-resolution RNA_SEGMENT_OUTPUT_RESOLUTION] [--num-workers NUM_WORKERS] [--metadata METADATA]
options:
-h, --help show this help message and exit
--image-in IMAGE_IN Key in the Open-ST h5 object (when --h5-in is specified) or path to the file where the mask will be loaded from
--h5-in H5_IN If specified, image is loaded from h5 (from key --image-in). Segmentation mask is saved there (to --mask-out). Default: ""
--mask-out MASK_OUT Key in the Open-ST h5 object (when --h5-in is specified) or path to the file where the mask will be written into
--rna-segment Performs segmentation based on local RNA density pseudoimages from sequencing data, instead of using a staining image. This assumes coordinates in microns (can be transformed with
--rna-segment-input-resolution)
--model MODEL cellpose model - either a path or a valid string to pretrained model. Default: ""
--flow-threshold FLOW_THRESHOLD
cellpose's 'flow_threshold' parameter. Default: 0.5
--cellprob-threshold CELLPROB_THRESHOLD
cellpose's 'cellprob_threshold' parameter. Default: 0
--diameter DIAMETER cellpose's 'diameter' parameter. Default: 20
--chunk-size CHUNK_SIZE
When prediction of the mask runs in separate chunks, this is the chunk square size (in pixels). Default: 512
--chunked If set, segmentation is computed at non-overlapping chunks of size '--chunk-size'
--max-image-pixels MAX_IMAGE_PIXELS
Upper bound for number of pixels in the images (prevents exception when opening very large images). Default: 933120000
--device {cpu,cuda} Device used to run the segmentation model. Can be ['cpu', 'cuda']. Default: "cpu"
--dilate-px DILATE_PX
Pixels the outlines of the segmentation mask will be extended. Default: 10
--outline-px OUTLINE_PX
Objects will be represented as px-width outlines (only if >0). Default: 0
--mask-tissue Tissue (imaging modality) is masked from the background before segmentation.
--tissue-masking-gaussian-sigma TISSUE_MASKING_GAUSSIAN_SIGMA
The gaussian blur sigma used during the isolation of the tissue on the staining image. Default: 5
--keep-black-background
Whether to set the background of the imaging modalities to white after tissue masking
--rna-segment-spatial-coord-key RNA_SEGMENT_SPATIAL_COORD_KEY
Path to the spatial coordinates inside the spatial object (e.g., 'obsm/spatial'). Default: "obsm/spatial"
--rna-segment-input-resolution RNA_SEGMENT_INPUT_RESOLUTION
Spatial resolution of the input coordinates (retrieved from --rna-segment-spatial-coord-key). If it is in microns, leave as 1. If it is in pixels, specify the pixel to micron conversion
factor. Default: 1
--rna-segment-render-scale RNA_SEGMENT_RENDER_SCALE
Size of bins for computing the binning (in microns). For Open-ST v1, we recommend a value of 2. Default: 2
--rna-segment-render-sigma RNA_SEGMENT_RENDER_SIGMA
Smoothing factor applied to the RNA pseudoimage (higher values lead to smoother images). Default: 1
--rna-segment-output-resolution RNA_SEGMENT_OUTPUT_RESOLUTION
Final resolution (micron/pixel) for the segmentation mask. Default: 0.6
--num-workers NUM_WORKERS
Number of CPU workers when --chunked is specified. Default: -1
--metadata METADATA Path where the metadata will be stored. If not specified, metadata is not saved. Warning: a report (via openst report) cannot be generated without metadata! Default: ""
segment_merge¶
Merge two segmentation masks into one
Usage:
openst segment_merge [-h] --h5-in H5_IN --mask-in MASK_IN MASK_IN --mask-out MASK_OUT [--chunk-size CHUNK_SIZE] [--chunked] [--num-workers NUM_WORKERS]
options:
-h, --help show this help message and exit
--h5-in H5_IN If set, masks are loaded from the Open-ST h5 object (key in --mask-in), and segmentation is saved there (to the key under --mask-out). Default: ""
--mask-in MASK_IN MASK_IN
Path to the input segmentation masks - two of them!
--mask-out MASK_OUT Path (file or h5) where the merged mask will be saved
--chunk-size CHUNK_SIZE
When prediction of the mask runs in separate chunks, this is the chunk square size (in pixels). Default: 512
--chunked If set, segmentation is computed at non-overlapping chunks of size '--chunk-size'
--num-workers NUM_WORKERS
Number of CPU workers when --chunked is specified. Default: -1
transcript_assign¶
Aggregate transcripts into segmented cells.
Usage:
openst transcript_assign [-h] --h5-in H5_IN --mask-in MASK_IN --spatial-key SPATIAL_KEY --h5-out H5_OUT [--mask-from-file] [--max-image-pixels MAX_IMAGE_PIXELS] [--shuffle-umi] [--metadata METADATA]
options:
-h, --help show this help message and exit
--h5-in H5_IN Path to an already aligned Open-ST h5 object
--mask-in MASK_IN Path to image mask - a key in the Open-ST h5 object. Or, can be an image stored separately in the filesystem (when --mask-from-file is specified) Image data and ST coordinates must be
pairwise aligned (implicit for the case of RNA-based segmentation)
--spatial-key SPATIAL_KEY
Key in the Open-ST h5 object where the aligned coordinates are stored, e.g. 'spatial_pairwise_aligned_coarse' (after using 'openst pairwise_aligner')
--h5-out H5_OUT Path where the segmented Open-ST h5 object will be written into
--mask-from-file If set, the image mask is loaded from an external file
--max-image-pixels MAX_IMAGE_PIXELS
Upper bound for number of pixels in the images (prevents exception when opening very large images). Default: 933120000
--shuffle-umi If set, UMI locations will be shuffled. This can be used as a baseline for feature selection.
--metadata METADATA Path where the metadata will be stored. If not specified, metadata is not saved. Warning: a report (via openst report) cannot be generated without metadata! Default: ""
pseudoimage¶
Generate pseudoimages of Open-ST RNA data and visualize using napari.
Usage:
openst pseudoimage [-h] --h5-in H5_IN [--spatial-coord-key SPATIAL_COORD_KEY] [--input-resolution INPUT_RESOLUTION] [--render-scale RENDER_SCALE] [--render-sigma RENDER_SIGMA]
[--output-resolution OUTPUT_RESOLUTION]
options:
-h, --help show this help message and exit
--h5-in H5_IN Necessary to create the pseudoimage
--spatial-coord-key SPATIAL_COORD_KEY
Path to the spatial coordinates inside the spatial object (e.g., 'obsm/spatial')
--input-resolution INPUT_RESOLUTION
Spatial resolution of the input coordinates (retrieved from --spatial-coord-key). If it is in microns, leave as 1. If it is in pixels, specify the pixel to micron conversion factor. Default: 1
--render-scale RENDER_SCALE
Size of bins for computing the binning (in microns). For Open-ST v1, we recommend a value of 2. Default: 2
--render-sigma RENDER_SIGMA
Smoothing factor applied to the RNA pseudoimage (higher values lead to smoother images). Default: 1
--output-resolution OUTPUT_RESOLUTION
Final resolution (micron/pixel) for the pseudoimage. Default: 0.6
preview¶
Preview locations (as points) and images of Open-ST data.
Usage:
openst preview [-h] --h5-in H5_IN [--file-structure] [--spatial-coord-keys SPATIAL_COORD_KEYS [SPATIAL_COORD_KEYS ...]] [--image-keys IMAGE_KEYS [IMAGE_KEYS ...]]
[--pseudoimage-keys PSEUDOIMAGE_KEYS [PSEUDOIMAGE_KEYS ...]] [--spatial-coord-resampling SPATIAL_COORD_RESAMPLING [SPATIAL_COORD_RESAMPLING ...]]
[--image-resampling IMAGE_RESAMPLING [IMAGE_RESAMPLING ...]] [--pseudoimage-units-to-um PSEUDOIMAGE_UNITS_TO_UM [PSEUDOIMAGE_UNITS_TO_UM ...]]
options:
-h, --help show this help message and exit
--h5-in H5_IN Necessary to create the pseudoimage
--file-structure If set, will not open a visualization screen but will return the tree structure of the h5 file
--spatial-coord-keys SPATIAL_COORD_KEYS [SPATIAL_COORD_KEYS ...]
Path to the spatial coordinates inside the spatial object (e.g., 'obsm/spatial'). Can be one or many (separated by space)
--image-keys IMAGE_KEYS [IMAGE_KEYS ...]
Path to the image to be visualized. Can be one or many (separated by space)
--pseudoimage-keys PSEUDOIMAGE_KEYS [PSEUDOIMAGE_KEYS ...]
Path to the spatial coordinates inside the spatial object to visualize as pseudoimage. Can be one or many (separated by space)
--spatial-coord-resampling SPATIAL_COORD_RESAMPLING [SPATIAL_COORD_RESAMPLING ...]
Will load every n-th point. Can be one (same for all spatial-coords) or many (1-to-1 mapping to the spatial-coord list). Default: [1]
--image-resampling IMAGE_RESAMPLING [IMAGE_RESAMPLING ...]
Will load every n-th pixel. Can be one (same for all images) or many (1-to-1 mapping to the image list). Default: [1]
--pseudoimage-units-to-um PSEUDOIMAGE_UNITS_TO_UM [PSEUDOIMAGE_UNITS_TO_UM ...]
Conversion factor from spatial units to micron, before rendering the pseudoimage. Can be one (same for all images) or many (1-to-1 mapping to the image list). Default: [1.0]
report¶
Generate HTML reports from metadata files (json).
Usage:
openst report [-h] --metadata METADATA --html-out HTML_OUT
options:
-h, --help show this help message and exit
--metadata METADATA Path to the metadata file (json)
--html-out HTML_OUT Path where the output HTML file will be created
from_spacemake¶
Run openst commands using spacemake file structure. You need to specify one subcommand from above, with the respective arguments.
Usage:
openst from_spacemake [-h] --project-id PROJECT_ID --sample-id SAMPLE_ID [--run-mode RUN_MODE] subcommand [params]
options:
-h, --help show this help message and exit
--project-id PROJECT_ID
From spacemake's project_df, this is the project_id string
--sample-id SAMPLE_ID
From spacemake's project_df, this is the sample_id string
--run-mode RUN_MODE When a sample has multiple run_mode(s), you must specify one
This command populates the arguments for the subcommands automatically. In the table below, you can find
which of this arguments are populated automatically. ... indicates that the value will change
depending on the --project-id and --sample-id configuration.
| subcommand | populated arguments |
|---|---|
spatial_stitch |
--h5-out ... --tiles ... --tile-id ... |
image_stitch |
--image-indir ... --image-out ... |
segment_merge |
--h5-in ... --mask-out uns/spatial/staining_image_mask_merged |
segment |
--h5-in ... --image-in uns/spatial/staining_image --mask-out uns/spatial/staining_image_mask |
transcript_assign |
--h5-in ... --mask-in uns/spatial/staining_image_mask --h5-out ... |
merge_modalities |
--h5-in ... --image-in ... |
manual_pairwise_aligner |
--h5-in ... |
apply_transform |
--h5-in ... |
pseudoimage |
--h5-in ... |
preview |
--h5-in ... |
pairwise_aligner |
--h5-in ... |
Note
You can override any of these values by providing them explicitly.