A python library to generate projects for MoBIE.
From conda:
$ conda install -c conda-forge mobie_utils
For development:
You can set up (and activate) a conda environment with all dependencies from environment.yaml
:
$ conda env create -f environment.yaml
$ conda activate mobie
and install the library via
$ pip install -e .
The library contains functionality to generate MoBIE projects, add data to it and create complex views. For complete examples, please check out the examples:
Below is a short code snippet that shows how to use it in a python script.
import mobie
# root folder for the mobie project
mobie_root = "/path/to/project-datasets/data"
# name of the dataset to be added
dataset_name = "my_dataset"
# file path and key for the input data
# key can be an internal path for hdf5 or zarr/n5 containers
# or a file pattern for image stacks
data_path = "/path/to/input_data.h5"
data_key = "/internal/h5/path"
# resolution of this initial data (in micrometer), chunks size and factors for downscaling
resolution = (.5, .25, .25)
chunks = (64, 128, 128)
scale_factors = [[1, 2, 2], [2, 2, 2], [2, 2, 2]]
mobie.add_image(data_path, data_key,
mobie_root, dataset_name, image_name,
resolution, chunks, scale_factors)
The package also installs some command line scripts that can create MoBIE projects, add data to it and more:
mobie.add_image
add image data to MoBIE dataset. Initialize the dataset if it does not exist yet.mobie.add_registered_source
apply registration in elastix format and add the resulting data to MoBIE dataset.mobie.add_segmentation
add segmentation image data to MoBIE dataset.mobie.add_traces
add data containing traces (= skeletonized objects).mobie.validate_project
validate that a MoBIE project follows the specmobie.validate_dataset
validate that a MoBIE dataset follows the specmobie.add_remote_metadata
adds the required metadata for accessing the data via s3.Run <COMMAND-NAME> --help
to get more information on how to use them.
This library also provides functionality to update MoBIE projects to new specification versions. Updating is performed with the command line function mobie.migrate_project
. Its only mandatory argument is the filepat to the project data:
mobie.migrate_project data
Warning: this command will update the metadata files without creating backups. You should either run this on projects within git, or create a manual backup of your project.
The most recent update is from version 0.2.1
to 0.3.0
. Previous version updates can be performed by passing the -v
flag to the migrate_project
command.
As most likely the specs for the project metadata files change during an update, you need to purge the cached specs files by deleting them in the .mobie
folder in your $HOME
directory.
If you use the MoBIE framework in your research, please cite the MoBIE publication.