manno Functions¶
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code.manno_getImage(server, token, channel, queryFile, fileOut, useSemaphore)¶ MANNO function to get OCP image data and format it to be compatible with ITK-Snap.
Inputs
- server: [string]
- OCP server name hosting the image data of interest
- token: [string]
- OCP token name for the annotation data of interest
- channel: [string]
- OCP channel name for the annotation data of interest
- queryFile: [string]
- path and filename for queryFile. Should be a MAT file containing one OCPQuery variable, named ‘query’
- fileOut: [string]
- path and filename for NIFTI image file to use in ITK Snap for annotating
- useSemaphore: [number][default=0]
- Throttles reading/writing client-side for large batch jobs. Not needed in single cutout mode
Outputs
No explicit outputs. Output file is saved to disk rather than output as a variable to allow for downstream integration with LONI.Notes
Currently only uint8 image data is supported. Multichannel data may produce unexpected results.
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code.manno_putAnno(server, token, channel, queryFile, fileIn, protoRAMON, doConnComp, useSemaphore)¶ MANNO function to upload annotation data from ITK-Snap to OCP.
Inputs
- server: [string]
- OCP server where annotation data will reside
- token: [string]
- OCP token name for the annotation data of interest
- channel: [string]
- OCP channel name for the annotation data of interest
- queryFile: [string]
- path and filename for queryFile. Should be a MAT file containing one OCPQuery variable, named ‘query’. This should be the same as the queryFile used to cutout data
- fileIn: [string]
- path and filename for NIFTI segmentation file saved in ITK Snap
- protoRAMON: [string]
- A prototype RAMONObject; each annotation object created will be based on this template (e.g., RAMONOrganelle, RAMONSynapse). Users can set fields (e.g., author, confidence) by writing wrapper scripts
- doConnComp: [number]
- If equal to 1, objects will be relabeled based on 3D (26-connected) voxels. If set to 0, objects will be uploaded exactly as created.
- useSemaphore: [number][default=0]
- Throttles reading/writing client-side for large batch jobs. Not needed in single cutout mode
Outputs
No explicit outputs. Output file is saved to disk rather than output as a variable to allow for downstream integration with LONI.Notes
Currently only uint8 image data is supported. Multichannel data may produce unexpected results.
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code.run_manno_example()¶ Manno Example manno starter to demonstrate protocol functionality. All required inputs are hardcoded for this demo. Paths are hardcoded for Linux/Mac.
This example should be run from the code directory because of the relative paths
The result of this run can be viewed in a webbrowser using the following URL: http://openconnecto.me/ocp/overlay/0.6/openconnecto.me/kasthuri11cc/image/openconnecto.me/manno/mito/xy/1/5472,5972/8712,9212/1031/
For questions on these functions, please contact Will Gray Roncal at wgr@jhu.edu