create_montage
This script can create a high-resolution montage of all images in a folder or datasets.
Create an overview image with thumbnails of all slides in a dataset.
usage: python create_montage.py --dataset <dataset_folder> --image_glob_pattern '**/*.tiff' --width 1000
Named Arguments
- --cluster
The name of the GPU or CPU cluster inside the AzureML workspacethat should execute the job. To run on your local machine, omit this argument.
Default: “”
- --datastore
The name of the AzureML datastore where the dataset is defined.
Default: “”
- --dataset
The name of the AzureML dataset to use for creating the montage. The dataset will be mounted automatically. Use an absolute path to a folder on the local machine to bypass mounting.
Default: “”
- --conda_env
The Conda environment file that should be used when submitting the present run to AzureML. If not specified, the hi-ml-cpath environment file will be used.
Default: hi-ml/hi-ml-cpath/environment.yml
- --wait_for_completion
If True, wait for AML Run to complete before proceeding. If False, submit the run to AML and exit
Default: False
- --docker_shm_size
The shared memory in the Docker image for the AzureML VMs.
Default: “100g”
- --workspace_config_path
The path to the AzureML workspace configuration file. If not specified, the configuration file in the current folder or one of its parents will be used.
- --display_name
The display name of the AzureML run. If not specified, a default name will be used.
Default: “”
- --level
Resolution downsample level, e.g. if lowest resolution is 40x and the available downsample levels are [1.0, 4.0, 16.0] then level = 1 corresponds to 10x magnification
Default: 1
- --exclude_by_slide_id
Provide a file that contains slide IDs that should be excluded. File format is CSV, the first column is used as the slide ID. If the file is empty, no slides will be excluded.
- --include_by_slide_id
Provide a file that contains slide IDs that should be included. File format is CSV, the first column is used as the slide ID. If the file is empty, no montage will be produced.
- --image_glob_pattern
When provided, use this pattern in rglob to find the files that should be included in the montage. Example: ‘**/*.tiff’ to find all TIFF files recursive. You may have to escape the pattern in your shell.
Default: “”
- --width
The width of the montage in pixels
Default: 60000
- --output_path
The folder where the montage will be saved
Default: outputs
- --parallel
The number of parallel processes to use when creating the montage.
Default: 8
- --backend
The backend to use for reading the slides. Can be ‘openslide’ or ‘cucim’
Default: “openslide”