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API of Open-ST tools

Here we show the description of all commands available in the openst tools, which can be run as:

openst <subcommand>

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 preprint.

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.