openapi: 3.0.3
info:
title: Girder REST API (Emory Digital Slide Archive) annotation slicer_cli_web API
version: 3.2.14
description: OpenAPI 3.0 conversion of the Girder REST API powering the Emory Digital Slide Archive (computablebrain). Converted faithfully from the live Swagger 2.0 document at https://computablebrain.emory.edu/api/v1/describe.
license:
name: Apache-2.0
url: https://www.apache.org/licenses/LICENSE-2.0.txt
servers:
- url: https://computablebrain.emory.edu/api/v1
tags:
- description: slicer_cli_web resource
name: slicer_cli_web
paths:
/slicer_cli_web/cli:
get:
operationId: slicer_cli_web_getItems_cli
parameters:
- name: folder
in: query
required: false
description: The base folder to look for tasks
schema:
type: string
responses:
'200':
description: Success
'403':
description: You are not logged in.
summary: List CLIs
tags:
- slicer_cli_web
/slicer_cli_web/cli/5f3d811c50cd9fe632566ecf/rerun:
post:
description: 'Rerun a previous job: Description: <br/><br/>Unmixes the stains of a composite image given the stain colors<br/><br/>Version: 0.2.0<br/><br/>License: Apache 2.0<br/><br/>Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)<br/><br/>Acknowledgements: This work is part of the HistomicsTK project.'
operationId: slicer_cli_web_rerunHandler_post_cli_5f3d811c50cd9fe632566ecf_rerun
parameters:
- name: jobId
in: query
required: true
description: The previous job ID
schema:
type: string
- name: inputImageFile
in: query
required: false
description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image to be deconvolved'
schema:
type: string
- name: inputImageFile_folder
in: query
required: false
description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image to be deconvolved'
schema:
type: string
- name: outputStainImageFile_1_folder
in: query
required: false
description: 'Girder ID of parent folder for output image - outputStainImageFile_1: Output Image of Stain 1 (*.tiff)'
schema:
type: string
- name: outputStainImageFile_1
in: query
required: false
description: 'Name of output image - outputStainImageFile_1: Output Image of Stain 1 (*.tiff)'
schema:
type: string
- name: outputStainImageFile_2_folder
in: query
required: false
description: 'Girder ID of parent folder for output image - outputStainImageFile_2: Output Image of Stain 2 (*.tiff)'
schema:
type: string
- name: outputStainImageFile_2
in: query
required: false
description: 'Name of output image - outputStainImageFile_2: Output Image of Stain 2 (*.tiff)'
schema:
type: string
- name: outputStainImageFile_3_folder
in: query
required: false
description: 'Girder ID of parent folder for output image - outputStainImageFile_3: Output Image of Stain 3 (*.tiff)'
schema:
type: string
- name: outputStainImageFile_3
in: query
required: false
description: 'Name of output image - outputStainImageFile_3: Output Image of Stain 3 (*.tiff)'
schema:
type: string
- name: outputAnnotationFile_folder
in: query
required: false
description: 'Girder ID of parent folder for output file - outputAnnotationFile: Annotation to relate images on source (*.anot)'
schema:
type: string
- name: outputAnnotationFile
in: query
required: false
description: 'Name of output file - outputAnnotationFile: Annotation to relate images on source (*.anot)'
schema:
type: string
- name: maxRegionSize
in: query
required: false
description: Maximum width and height allowed when processing an image, in order to prevent accidentally running on too large a region. Use -1 for no limit
schema:
type: integer
format: int32
- name: region
in: query
required: false
description: left,top,width,height of the region of interest. All -1 means the whole image is used. as JSON (region)
schema:
type: string
- name: stain_1
in: query
required: false
description: Name of stain-1
schema:
type: string
enum:
- hematoxylin
- eosin
- dab
- custom
- name: stain_1_vector
in: query
required: false
description: Custom value for stain-1 as JSON (double-vector)
schema:
type: string
- name: stain_2
in: query
required: false
description: Name of stain-2
schema:
type: string
enum:
- hematoxylin
- eosin
- dab
- custom
- 'null'
- name: stain_2_vector
in: query
required: false
description: Custom value for stain-2 as JSON (double-vector)
schema:
type: string
- name: stain_3
in: query
required: false
description: Name of stain-3
schema:
type: string
enum:
- hematoxylin
- eosin
- dab
- 'null'
- custom
- name: stain_3_vector
in: query
required: false
description: Custom value for stain-3 as JSON (double-vector)
schema:
type: string
responses:
'200':
description: Success
'400':
description: A parameter was invalid.
summary: Rerun Color Deconvolution
tags:
- slicer_cli_web
/slicer_cli_web/cli/5f3d811c50cd9fe632566ecf/run:
post:
description: 'Description: <br/><br/>Unmixes the stains of a composite image given the stain colors<br/><br/>Version: 0.2.0<br/><br/>License: Apache 2.0<br/><br/>Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)<br/><br/>Acknowledgements: This work is part of the HistomicsTK project.'
operationId: slicer_cli_web_cliHandler_post_cli_5f3d811c50cd9fe632566ecf_run
parameters:
- name: inputImageFile
in: query
required: true
description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image to be deconvolved'
schema:
type: string
- name: inputImageFile_folder
in: query
required: false
description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image to be deconvolved'
schema:
type: string
- name: outputStainImageFile_1_folder
in: query
required: true
description: 'Girder ID of parent folder for output image - outputStainImageFile_1: Output Image of Stain 1 (*.tiff)'
schema:
type: string
- name: outputStainImageFile_1
in: query
required: true
description: 'Name of output image - outputStainImageFile_1: Output Image of Stain 1 (*.tiff)'
schema:
type: string
default: outputStainImageFile_1.tiff
- name: outputStainImageFile_2_folder
in: query
required: true
description: 'Girder ID of parent folder for output image - outputStainImageFile_2: Output Image of Stain 2 (*.tiff)'
schema:
type: string
- name: outputStainImageFile_2
in: query
required: true
description: 'Name of output image - outputStainImageFile_2: Output Image of Stain 2 (*.tiff)'
schema:
type: string
default: outputStainImageFile_2.tiff
- name: outputStainImageFile_3_folder
in: query
required: true
description: 'Girder ID of parent folder for output image - outputStainImageFile_3: Output Image of Stain 3 (*.tiff)'
schema:
type: string
- name: outputStainImageFile_3
in: query
required: true
description: 'Name of output image - outputStainImageFile_3: Output Image of Stain 3 (*.tiff)'
schema:
type: string
default: outputStainImageFile_3.tiff
- name: outputAnnotationFile_folder
in: query
required: false
description: 'Girder ID of parent folder for output file - outputAnnotationFile: Annotation to relate images on source (*.anot)'
schema:
type: string
- name: outputAnnotationFile
in: query
required: false
description: 'Name of output file - outputAnnotationFile: Annotation to relate images on source (*.anot)'
schema:
type: string
default: outputAnnotationFile.anot
- name: maxRegionSize
in: query
required: false
description: Maximum width and height allowed when processing an image, in order to prevent accidentally running on too large a region. Use -1 for no limit
schema:
type: integer
format: int32
default: 5000
- name: region
in: query
required: false
description: left,top,width,height of the region of interest. All -1 means the whole image is used. as JSON (region)
schema:
type: string
default: '[-1.0, -1.0, -1.0, -1.0]'
- name: stain_1
in: query
required: false
description: Name of stain-1
schema:
type: string
enum:
- hematoxylin
- eosin
- dab
- custom
default: hematoxylin
- name: stain_1_vector
in: query
required: false
description: Custom value for stain-1 as JSON (double-vector)
schema:
type: string
default: '[-1.0, -1.0, -1.0]'
- name: stain_2
in: query
required: false
description: Name of stain-2
schema:
type: string
enum:
- hematoxylin
- eosin
- dab
- custom
- 'null'
default: eosin
- name: stain_2_vector
in: query
required: false
description: Custom value for stain-2 as JSON (double-vector)
schema:
type: string
default: '[-1.0, -1.0, -1.0]'
- name: stain_3
in: query
required: false
description: Name of stain-3
schema:
type: string
enum:
- hematoxylin
- eosin
- dab
- 'null'
- custom
default: 'null'
- name: stain_3_vector
in: query
required: false
description: Custom value for stain-3 as JSON (double-vector)
schema:
type: string
default: '[-1.0, -1.0, -1.0]'
responses:
'200':
description: Success
'400':
description: A parameter was invalid.
summary: Color Deconvolution
tags:
- slicer_cli_web
/slicer_cli_web/cli/5f3d811c50cd9fe632566ed1/rerun:
post:
description: 'Rerun a previous job: Description: <br/><br/>Use sparse non-negative matrix factorization to adaptively deconvolve a given RGB image into intensity images representing distinct stains.<br/><br/>Version: 0.1.0<br/><br/>License: Apache 2.0<br/><br/>Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)<br/><br/>Acknowledgements: This work is part of the HistomicsTK project.'
operationId: slicer_cli_web_rerunHandler_post_cli_5f3d811c50cd9fe632566ed1_rerun
parameters:
- name: jobId
in: query
required: true
description: The previous job ID
schema:
type: string
- name: sample_slide_path
in: query
required: false
description: 'Girder ID of input image (if batch input, this is a regex for item names) - sample_slide_path: Input image to be deconvolved'
schema:
type: string
- name: sample_slide_path_folder
in: query
required: false
description: 'Girder ID of parent folder for batch input image - sample_slide_path: Input image to be deconvolved'
schema:
type: string
- name: snmf_I_0
in: query
required: false
description: Background intensity in each channel as JSON (double-vector)
schema:
type: string
- name: outputAnnotationFile_folder
in: query
required: false
description: 'Girder ID of parent folder for output file - outputAnnotationFile: Output stain annotation file (*.anot)'
schema:
type: string
- name: outputAnnotationFile
in: query
required: false
description: 'Name of output file - outputAnnotationFile: Output stain annotation file (*.anot)'
schema:
type: string
- name: snmf_beta
in: query
required: false
description: A parameter to control sparsity of stain concentrations
schema:
type: number
format: double
- name: sample_magnification
in: query
required: false
description: Desired magnification for sampling. The default value indicates native scan magnification.
schema:
type: number
format: float
- name: sample_min_coverage
in: query
required: false
description: "Minimum background coverage required for a tile to\n be sampled from."
schema:
type: number
format: float
- name: sample_sample_approximate_total
in: query
required: false
description: Use instead of sample_fraction to specify roughly how many pixels to sample. The fewer tiles are excluded, the more accurate this will be.
schema:
type: integer
format: int32
- name: sample_sample_fraction
in: query
required: false
description: Fraction of pixels to sample. Specify either this or --sampleApproximateTotal
schema:
type: number
format: float
- name: dask_scheduler
in: query
required: false
description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode.
schema:
type: string
- name: sample_tissue_seg_mag
in: query
required: false
description: Low resolution magnification at which foreground and background will be segmented.
schema:
type: number
format: float
- name: stains_stain_1
in: query
required: false
description: Name for initial estimate of color of stain-1
schema:
type: string
enum:
- hematoxylin
- eosin
- dab
- custom
- name: stains_stain_1_vector
in: query
required: false
description: Custom value for initial estimate of stain-1 as JSON (double-vector)
schema:
type: string
- name: stains_stain_2
in: query
required: false
description: Name for initial estimate of color of stain-2
schema:
type: string
enum:
- hematoxylin
- eosin
- dab
- custom
- name: stains_stain_2_vector
in: query
required: false
description: Custom value for initial estimate of stain-2 as JSON (double-vector)
schema:
type: string
- name: sample_tile_grouping
in: query
required: false
description: Number of tiles to process as part of a single task
schema:
type: integer
format: int32
responses:
'200':
description: Success
'400':
description: A parameter was invalid.
summary: Rerun Adaptive Color Deconvolution
tags:
- slicer_cli_web
/slicer_cli_web/cli/5f3d811c50cd9fe632566ed1/run:
post:
description: 'Description: <br/><br/>Use sparse non-negative matrix factorization to adaptively deconvolve a given RGB image into intensity images representing distinct stains.<br/><br/>Version: 0.1.0<br/><br/>License: Apache 2.0<br/><br/>Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)<br/><br/>Acknowledgements: This work is part of the HistomicsTK project.'
operationId: slicer_cli_web_cliHandler_post_cli_5f3d811c50cd9fe632566ed1_run
parameters:
- name: sample_slide_path
in: query
required: true
description: 'Girder ID of input image (if batch input, this is a regex for item names) - sample_slide_path: Input image to be deconvolved'
schema:
type: string
- name: sample_slide_path_folder
in: query
required: false
description: 'Girder ID of parent folder for batch input image - sample_slide_path: Input image to be deconvolved'
schema:
type: string
- name: snmf_I_0
in: query
required: true
description: Background intensity in each channel as JSON (double-vector)
schema:
type: string
default: '[255.0, 255.0, 255.0]'
- name: outputAnnotationFile_folder
in: query
required: true
description: 'Girder ID of parent folder for output file - outputAnnotationFile: Output stain annotation file (*.anot)'
schema:
type: string
- name: outputAnnotationFile
in: query
required: true
description: 'Name of output file - outputAnnotationFile: Output stain annotation file (*.anot)'
schema:
type: string
default: outputAnnotationFile.anot
- name: snmf_beta
in: query
required: false
description: A parameter to control sparsity of stain concentrations
schema:
type: number
format: double
default: 0.5
- name: sample_magnification
in: query
required: false
description: Desired magnification for sampling. The default value indicates native scan magnification.
schema:
type: number
format: float
default: -1.0
- name: sample_min_coverage
in: query
required: false
description: "Minimum background coverage required for a tile to\n be sampled from."
schema:
type: number
format: float
default: 0.1
- name: sample_sample_approximate_total
in: query
required: false
description: Use instead of sample_fraction to specify roughly how many pixels to sample. The fewer tiles are excluded, the more accurate this will be.
schema:
type: integer
format: int32
default: -1
- name: sample_sample_fraction
in: query
required: false
description: Fraction of pixels to sample. Specify either this or --sampleApproximateTotal
schema:
type: number
format: float
default: 0.1
- name: dask_scheduler
in: query
required: false
description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode.
schema:
type: string
default: ''
- name: sample_tissue_seg_mag
in: query
required: false
description: Low resolution magnification at which foreground and background will be segmented.
schema:
type: number
format: float
default: 1.25
- name: stains_stain_1
in: query
required: false
description: Name for initial estimate of color of stain-1
schema:
type: string
enum:
- hematoxylin
- eosin
- dab
- custom
default: hematoxylin
- name: stains_stain_1_vector
in: query
required: false
description: Custom value for initial estimate of stain-1 as JSON (double-vector)
schema:
type: string
default: '[-1.0, -1.0, -1.0]'
- name: stains_stain_2
in: query
required: false
description: Name for initial estimate of color of stain-2
schema:
type: string
enum:
- hematoxylin
- eosin
- dab
- custom
default: eosin
- name: stains_stain_2_vector
in: query
required: false
description: Custom value for initial estimate of stain-2 as JSON (double-vector)
schema:
type: string
default: '[-1.0, -1.0, -1.0]'
- name: sample_tile_grouping
in: query
required: false
description: Number of tiles to process as part of a single task
schema:
type: integer
format: int32
default: 256
responses:
'200':
description: Success
'400':
description: A parameter was invalid.
summary: Adaptive Color Deconvolution
tags:
- slicer_cli_web
/slicer_cli_web/cli/5f3d811c50cd9fe632566ed3/rerun:
post:
description: 'Rerun a previous job: Description: <br/><br/>Detects nuclei in a whole-slide image<br/><br/>Version: 0.1.0<br/><br/>License: Apache 2.0<br/><br/>Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)<br/><br/>Acknowledgements: This work is part of the HistomicsTK project.'
operationId: slicer_cli_web_rerunHandler_post_cli_5f3d811c50cd9fe632566ed3_rerun
parameters:
- name: jobId
in: query
required: true
description: The previous job ID
schema:
type: string
- name: inputImageFile
in: query
required: false
description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image'
schema:
type: string
- name: inputImageFile_folder
in: query
required: false
description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image'
schema:
type: string
- name: outputNucleiAnnotationFile_folder
in: query
required: false
description: 'Girder ID of parent folder for output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)'
schema:
type: string
- name: outputNucleiAnnotationFile
in: query
required: false
description: 'Name of output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)'
schema:
type: string
- name: analysis_mag
in: query
required: false
description: The magnification at which the analysis should be performed.
schema:
type: number
format: double
- name: analysis_roi
in: query
required: false
description: Region of interest within which the analysis should be done. Must be a four element vector in the format "left, top, width, height" in the space of the base layer. Default value of "-1, -1, -1, -1" indicates that the whole image should be processed. as JSON (region)
schema:
type: string
- name: analysis_tile_size
in: query
required: false
description: Tile size for blockwise analysis
schema:
type: number
format: double
- name: foreground_threshold
in: query
required: false
description: Intensity value to use as threshold to segment foreground in nuclear stain image
schema:
type: number
format: double
- name: frame
in: query
required: false
description: Frame index in a multi-frame image
schema:
type: string
- name: ignore_border_nuclei
in: query
required: false
description: Ignore/drop nuclei touching the image/tile border
schema:
type: boolean
- name: ImageInversionForm
in: query
required: false
description: Image inversion may be needed for greyscale images with bright nuclei and dark background. default option will automatically invert the image if it is single channel. Choose if color inversion is needed.
schema:
type: string
enum:
- 'Yes'
- 'No'
- default
- name: local_max_search_radius
in: query
required: false
description: Local max search radius used for detection seed points in nuclei
schema:
type: number
format: double
- name: max_radius
in: query
required: false
description: Maximum nuclear radius (used to set max sigma of the multiscale LoG filter)
schema:
type: number
format: double
- name: min_fgnd_frac
in: query
required: false
description: The minimum amount of foreground that must be present in a tile for it to be analyzed
schema:
type: number
format: double
- name: min_nucleus_area
in: query
required: false
description: Minimum area that each nucleus should have
schema:
type: integer
format: int32
- name: min_radius
in: query
required: false
description: Minimum nuclear radius (used to set min sigma of the multiscale LoG filter)
schema:
type: number
format: double
- name: nuclei_annotation_format
in: query
required: false
description: Format of the output nuclei annotations
schema:
type: string
enum:
- bbox
- boundary
- name: num_threads_per_worker
in: query
required: false
description: Number of threads to use per worker while setting up a local cluster internally. Must be a positive integer >= 1.
schema:
type: integer
format: int32
- name: num_workers
in: query
required: false
description: Number of dask workers to start while setting up a local cluster internally. If a negative value is specified then the number of workers is set to number of cpu cores on the machine minus the number of workers specified.
schema:
type: integer
format: int32
- name: reference_mu_lab
in: query
required: false
description: Mean of reference image in LAB color space for Reinhard color normalization as JSON (double-vector)
schema:
type: string
- name: reference_std_lab
in: query
required: false
description: Standard deviation of reference image in LAB color space for Reinhard color normalization as JSON (double-vector)
schema:
type: string
- name: remove_overlapping_nuclei_segmentation
in: query
required: false
description: Remove overlapping nuclei segmentation from the given region. It is recommended to use this approach when defining the tile overlap parameter.
schema:
type: boolean
- name: scheduler
in: query
required: false
description: Address of a dask scheduler in the format '127.0.0.1:8786'. Not passing this parameter sets up a dask cluster on the local machine. 'multiprocessing' uses Python multiprocessing. 'multithreading' uses Python multiprocessing in threaded mode.
schema:
type: string
- name: stain_1
in: query
required: false
description: Name of stain-1
schema:
type: string
enum:
- hematoxylin
- eosin
- dab
- custom
- name: stain_1_vector
in: query
required: false
description: Custom value for stain-1 as JSON (double-vector)
schema:
type: string
- name: stain_2
in: query
required: false
description: Name of stain-2
schema:
type: string
enum:
- hematoxylin
- eosin
- dab
- custom
- name: stain_2_vector
in: query
required: false
description: Custom value for stain-2 as JSON (double-vector)
schema:
type: string
- name: stain_3
in: query
required: false
description: Name of stain-3
schema:
type: string
enum:
- hematoxylin
- eosin
- dab
- 'null'
- custom
- name: stain_3_vector
in: query
required: false
description: Custom value for stain-3 as JSON (double-vector)
schema:
type: string
- name: style
in: query
required: false
description: Image style options for compositing a multi-frame image
schema:
type: string
- name: tile_overlap_value
in: query
required: false
description: Tile overlap size in pixels, Default value of -1 indicate that the tile overlap will be set to (max_radius + 1) * 4
schema:
type: integer
format: int32
responses:
'200':
description: Success
'400':
description: A parameter was invalid.
summary: Rerun Detects Nuclei
tags:
- slicer_cli_web
/slicer_cli_web/cli/5f3d811c50cd9fe632566ed3/run:
post:
description: 'Description: <br/><br/>Detects nuclei in a whole-slide image<br/><br/>Version: 0.1.0<br/><br/>License: Apache 2.0<br/><br/>Author(s): Deepak Roy Chittajallu (Kitware), Neal Siekierski (Kitware)<br/><br/>Acknowledgements: This work is part of the HistomicsTK project.'
operationId: slicer_cli_web_cliHandler_post_cli_5f3d811c50cd9fe632566ed3_run
parameters:
- name: inputImageFile
in: query
required: true
description: 'Girder ID of input image (if batch input, this is a regex for item names) - inputImageFile: Input image'
schema:
type: string
- name: inputImageFile_folder
in: query
required: false
description: 'Girder ID of parent folder for batch input image - inputImageFile: Input image'
schema:
type: string
- name: outputNucleiAnnotationFile_folder
in: query
required: true
description: 'Girder ID of parent folder for output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)'
schema:
type: string
- name: outputNucleiAnnotationFile
in: query
required: true
description: 'Name of output file - outputNucleiAnnotationFile: Output nuclei annotation file (*.anot)'
schema:
type: string
default: outputNucleiAnnotationFile.anot
- name: analysis_mag
in: query
required: false
description: The magnification at which the analysis should be performed.
schema:
type: number
format: double
default: 20.0
- name: analysis_roi
in: query
required: false
description: Region of interest within which the analysis should be done. Must be a four element vector in the format "left, top, width, height" in the space of the base layer. Default value of "-1, -1, -1, -1" indicates that the whole image should be processed. as JSON (region)
schema:
type: string
default: '[-1.0, -1.0, -1.0, -1.0]'
- name: analysis_tile_size
in: query
required: false
description: Tile size for blockwise analysis
schema:
type: number
format: double
default: 1024.0
- name: foreground_threshold
in: query
required: fals
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# Full source: https://raw.githubusercontent.com/api-evangelist/emory/refs/heads/main/openapi/emory-slicer-cli-web-api-openapi.yml