aliby.io.omero.Image¶
- class Image(image_id, **server_info)[source]¶
Bases:
BridgeOmero
Loads images from OMERO and gives access to the data and metadata.
- Attributes
- data
- file_annotations
metadata
Store metadata saved in OMERO: image size, number of time points, labels of channels, and image name.
- name
- ome_class
Methods
add_file_as_annotation
(file_to_upload, **kwargs)Upload annotation to object on OMERO server.
from_h5
(filepath)Instatiate Image from a hdf5 file.
server_info_from_h5
(filepath)Return server info from hdf5 file.
create_gate
set_id
Establishes the connection to the OMERO server via the Argo base class.
- Parameters
- image_id: integer
- server_info: dictionary
Specifies the host, username, and password as strings
- Attributes
- data
- file_annotations
metadata
Store metadata saved in OMERO: image size, number of time points, labels of channels, and image name.
- name
- ome_class
Methods
add_file_as_annotation
(file_to_upload, **kwargs)Upload annotation to object on OMERO server.
from_h5
(filepath)Instatiate Image from a hdf5 file.
server_info_from_h5
(filepath)Return server info from hdf5 file.
create_gate
set_id
- __init__(image_id, **server_info)[source]¶
Establishes the connection to the OMERO server via the Argo base class.
- Parameters
- image_id: integer
- server_info: dictionary
Specifies the host, username, and password as strings
Methods
__init__
(image_id, **server_info)Establishes the connection to the OMERO server via the Argo base class.
add_file_as_annotation
(file_to_upload, **kwargs)Upload annotation to object on OMERO server.
create_gate
()- rtype
bool
from_h5
(filepath)Instatiate Image from a hdf5 file.
server_info_from_h5
(filepath)Return server info from hdf5 file.
set_id
(ome_id)Attributes
data
file_annotations
Store metadata saved in OMERO: image size, number of time points, labels of channels, and image name.
name
ome_class
- add_file_as_annotation(file_to_upload, **kwargs)¶
Upload annotation to object on OMERO server. Only valid in subclasses.
- Parameters
- file_to_upload: File to upload
- **kwargs: Additional keyword arguments passed on
to BlitzGateway.createFileAnnfromLocalFile
- classmethod from_h5(filepath)[source]¶
Instatiate Image from a hdf5 file.
- Parameters
- clsImage
Image class
- filepatht.Union[str, PosixPath]
Location of hdf5 file.
Examples
FIXME: Add docs.
- property metadata¶
Store metadata saved in OMERO: image size, number of time points, labels of channels, and image name.
- classmethod server_info_from_h5(filepath)¶
Return server info from hdf5 file.
- Parameters
- clsBridgeOmero
BridgeOmero class
- filepatht.Union[str, PosixPath]
Location of hdf5 file.
Examples
FIXME: Add docs.