Convert Images¶
The conversion commands allow you to transform various types of images or image stacks into the WEBKNOSSOS dataset format. Each command is tailored for a specific input dataset type, ensuring efficient and accurate conversion. Below is an overview of the available commands and their usage.
Available Commands¶
convert
: Converts an image stack to a WEBKNOSSOS dataset.convert-raw
: Converts a RAW dataset to a WEBKNOSSOS dataset.convert-knossos
: Converts a KNOSSOS dataset to a WEBKNOSSOS dataset.convert-zarr
: Converts a Zarr dataset to a WEBKNOSSOS dataset.
convert
¶
The convert
command automatically detects an image stack and converts it into a WEBKNOSSOS dataset.
Supported input formats¶
- Standard image formats, e.g.
tiff
,jpg
,png
,bmp
- Proprietary image formats, e.g.
dm3
- Raw binary files
Usage¶
webknossos convert [OPTIONS] SOURCE TARGET
Arguments¶
-
SOURCE
Path to the source image stack.
Example:/path/to/source/images
. -
TARGET
Path to the target WEBKNOSSOS dataset.
Example:/path/to/target/dataset
.
Options¶
-
--voxel-size
The size of one voxel in the source data in nanometers.
Example:--voxel-size 11.0,11.0,20.0
. -
--unit
The unit of the voxel size.
Default:nanometers
. -
--layer-name
Name of the layer to be created.
Default:None
. -
--data-format
Data format to store the target dataset.
Options:wkw
,zarr
,zarr3
Default:zarr3
. -
--chunk-shape
Number of voxels to be stored as a chunk in the output format.
Example:--chunk-shape 32,32,32
. -
--shard-shape
Number of voxels to be stored as a shard in the output format.
Example:--shard-shape 1024,1024,1024
. -
--compress
Enable compression of the target dataset.
Default:True
. -
--downsample
Downsample the target dataset. Default:True
. -
--max-mag
Create downsampled magnifications up to the magnification specified by this argument. If omitted, the coarsest magnification will be determined by using the bounding box of the layer Example:--max-mag 2-2-1
. -
--interpolation-mode
The interpolation mode that should be used. Options:median
,mode
,nearest
,bilinear
,bicubic
. Default:default
(=mode
for segmentation,median
for color). -
--sampling-mode
The sampling mode to use. Options:anisotropic
,isotropic
,constant_z
. Default:anisotropic
. -
--overwrite-existing
Clear target folder, if it already exists. Not enabled by default. Use with caution. -
--jobs
Number of processes to be spawned for parallel execution.
Default: Number of CPU cores. -
--distribution-strategy
Strategy to distribute the task across CPUs or nodes.
Options:multiprocessing
,slurm
,kubernetes
,sequential
. Default:multiprocessing
. -
--batch-size
Number of images to be processed in one batch (influences RAM consumption). When creating a WKW dataset, batch-size must be a multiple of chunk-shape's z dimension. When converting to Zarr or Zarr3, batch-size must be a multiple of the z dimension of the shard shape (chunk-shape x chunks-per-shard). Default: None (= z dimension of shard-shape).
Example Commands¶
Convert an image stack locally:
webknossos convert /path/to/source/images /path/to/target/dataset
Convert an image stack using parallel execution:
webknossos convert --jobs 4 /path/to/source/images /path/to/target/dataset
convert-raw
¶
The convert-raw
command converts a RAW dataset into a WEBKNOSSOS dataset.
Usage¶
webknossos convert-raw [OPTIONS] SOURCE TARGET
Arguments¶
-
SOURCE
Path to the source RAW dataset.
Example:/path/to/source/raw
. -
TARGET
Path to the target WEBKNOSSOS dataset.
Example:/path/to/target/dataset
.
Options¶
-
--shape
Shape of the source dataset.
Example:--shape 1024,1024,512
. -
--voxel-size
The size of one voxel in the source data in nanometers.
Example:--voxel-size 11.0,11.0,20.0
. -
--unit
The unit of the voxel size.
Default:nanometers
. -
--dtype
Target datatype (e.g.,uint8
,uint16
,uint32
).
Default:uint8
. -
--source-dtype
Source datatype (e.g.,uint8
,uint16
,uint32
).
If omitted, it is assumed to be the same as the target datatype. -
--order
Input data storage layout:C
(row-major) orF
(column-major).
Default:F
. -
--layer-name
Name of the layer to be created.
Default:color
. -
--rescale-min-max
Rescale the values of the target dataset by specifying the min and max values. Will be scaled to the range from 0 to the maximum value of the target data type or 1.0 for floats. Example:--rescale-min-max 0.2,0.8
. -
--flip-axes
The axes at which should be flipped. Input format is a comma-separated list of axis indices. For example, 1,2,3 will flip the x, y and z axes. -
--data-format
Data format to store the target dataset. Options:wkw
,zarr
,zarr3
Default:zarr3
. -
--chunk-shape
Number of voxels to be stored as a chunk in the output format.
Example:--chunk-shape 32,32,32
. -
--shard-shape
Number of voxels to be stored as a shard in the output format.
Example:--shard-shape 1024,1024,1024
. -
--compress
Enable compression of the target dataset.
Default:True
. -
--downsample
Downsample the target dataset. Default:True
. -
--max-mag
Create downsampled magnifications up to the magnification specified by this argument. If omitted, the coarsest magnification will be determined by using the bounding box of the layer Example:--max-mag 2-2-1
. -
--interpolation-mode
The interpolation mode that should be used. Options:median
,mode
,nearest
,bilinear
,bicubic
. Default:default
(=mode
for segmentation,median
for color). -
--sampling-mode
The sampling mode to use. Options:anisotropic
,isotropic
,constant_z
. Default:anisotropic
. -
--overwrite-existing
Clear target folder, if it already exists. Not enabled by default. Use with caution. -
--jobs
Number of processes to be spawned for parallel execution.
Default: Number of CPU cores. -
--distribution-strategy
Strategy to distribute the task across CPUs or nodes.
Options:multiprocessing
,slurm
,kubernetes
,sequential
. Default:multiprocessing
.
Example Commands¶
Convert a RAW dataset locally:
webknossos convert-raw --shape 1024,1024,512 /path/to/source/raw /path/to/target/dataset
Convert a RAW dataset using parallel execution:
webknossos convert-raw --shape 1024,1024,512 --jobs 4 /path/to/source/raw /path/to/target/dataset
convert-knossos
¶
The convert-knossos
command converts a KNOSSOS dataset into a WEBKNOSSOS dataset.
Usage¶
webknossos convert-knossos [OPTIONS] SOURCE TARGET
Arguments¶
-
SOURCE
Path to the source KNOSSOS dataset.
Example:/path/to/source/knossos
. -
TARGET
Path to the target WEBKNOSSOS dataset.
Example:/path/to/target/dataset
.
Options¶
-
--voxel-size
The size of one voxel in the source data in nanometers.
Example:--voxel-size 11.0,11.0,20.0
. -
--unit
The unit of the voxel size.
Default:nanometers
. -
--layer-name
Name of the layer to be created.
Default:color
. -
--dtype
Target datatype (e.g.,uint8
,uint16
,uint32
).
Default:uint8
. -
--data-format
Data format to store the target dataset.
Options:wkw
,zarr
,zarr3
Default:zarr3
-
--chunk-shape
Number of voxels to be stored as a chunk in the output format.
Example:--chunk-shape 32,32,32
. -
--shard-shape
Number of voxels to be stored as a shard in the output format.
Example:--shard-shape 1024,1024,1024
. -
--jobs
Number of processes to be spawned for parallel execution.
Default: Number of CPU cores. -
--distribution-strategy
Strategy to distribute the task across CPUs or nodes.
Options:multiprocessing
,slurm
,kubernetes
,sequential
. Default:multiprocessing
.
Example Commands¶
Convert a KNOSSOS dataset locally:
webknossos convert-knossos /path/to/source/knossos /path/to/target/dataset
Convert a KNOSSOS dataset with custom voxel size and parallel execution:
webknossos convert-knossos --voxel-size 11.0,11.0,20.0 --jobs 4 /path/to/source/knossos /path/to/target/dataset
convert-zarr
¶
The convert-zarr
command converts a Zarr dataset into a WEBKNOSSOS dataset.
Usage¶
webknossos convert-zarr [OPTIONS] SOURCE TARGET
Arguments¶
-
SOURCE
Path to the source Zarr dataset.
Example:/path/to/source/zarr
. -
TARGET
Path to the target WEBKNOSSOS dataset.
Example:/path/to/target/dataset
.
Options¶
-
--voxel-size
The size of one voxel in the source data in nanometers.
Example:--voxel-size 11.0,11.0,20.0
. -
--unit
The unit of the voxel size.
Default:nanometers
. -
--layer-name
Name of the layer to be created.
Default:color
. -
--is-segmentation-layer
When converting one layer, signals whether layer is segmentation layer. When converting a folder, this option is ignored. -
--data-format
Data format to store the target dataset. Options:wkw
,zarr
,zarr3
Default:zarr3
. -
--chunk-shape
Number of voxels to be stored as a chunk in the output format.
Example:--chunk-shape 32,32,32
. -
--shard-shape
Number of voxels to be stored as a shard in the output format.
Example:--shard-shape 1024,1024,1024
. -
--flip-axes
The axes at which should be flipped. Input format is a comma-separated list of axis indices. For example, 1,2,3 will flip the x, y and z axes. -
--compress
Enable compression of the target dataset.
Default:True
. -
--downsample
Downsample the target dataset. Default:True
. -
--max-mag
Create downsampled magnifications up to the magnification specified by this argument. If omitted, the coarsest magnification will be determined by using the bounding box of the layer Example:--max-mag 2-2-1
. -
--interpolation-mode
The interpolation mode that should be used. Options:median
,mode
,nearest
,bilinear
,bicubic
. Default:default
(=mode
for segmentation,median
for color). -
--sampling-mode
The sampling mode to use. Options:anisotropic
,isotropic
,constant_z
. Default:anisotropic
. -
--overwrite-existing
Clear target folder, if it already exists. Not enabled by default. Use with caution. -
--jobs
Number of processes to be spawned for parallel execution.
Default: Number of CPU cores. -
--distribution-strategy
Strategy to distribute the task across CPUs or nodes.
Options:multiprocessing
,slurm
,kubernetes
,sequential
. Default:multiprocessing
.
Example Commands¶
Convert a Zarr dataset locally:
webknossos convert-zarr /path/to/source/zarr /path/to/target/dataset
Convert a Zarr dataset using parallel execution:
webknossos convert-zarr --jobs 4 /path/to/source/zarr /path/to/target/dataset
Convert a Zarr dataset using SLURM with custom job resources:
webknossos convert-zarr --distribution-strategy slurm --job-resources '{"mem": "10M"}' /path/to/source/zarr /path/to/target/dataset
Notes¶
- Ensure that the source and target paths are accessible and properly configured.
- Use the
--jobs
option to optimize performance for large datasets. - For distributed execution, configure the
--distribution-strategy
and related options. - Adjust options as needed to match your dataset specifications and desired output configuration.
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