Learn R Programming

romero.gateway (version 0.4.4)

OMERO R Gateway

Description

R Wrapper around the OMERO Java Gateway, which enables access to an OMERO server within R. Supported OMERO version: 5.4 .

Copy Link

Version

Install

install.packages('romero.gateway')

Monthly Downloads

10

Version

0.4.4

License

GPL (>= 2)

Issues

6

Pull Requests

1

Stars

6

Forks

10

Maintainer

Dominik Lindner

Last Published

December 23rd, 2018

Functions in romero.gateway (0.4.4)

attachDataframe,OMERO-method

Attaches a dataframe to an OME object
Image-class

Image
cast,OMERO-method

Casts a general OMERO object into its proper type, e. g. Plate (if possible)
cast

Casts a general OMERO object into its proper type, e. g. Plate (if possible)
getImages,Screen-method

Get all images of a screen
getOMEROType

Get the type of the OME object
getScreens

Get all screens of the logged in user
getThumbnail,Image-method

Get the thumbnail for an Image (as JPEG)
getImages,Project-method

Get all images of a project
getOMEROType,OMERO-method

Get the type of the OME object
attachFile,OMERO-method

Attach a file to an OME object
loadDataframe,OMERO-method

Load a dataframe attached to an OME object
availableDataframes,OMERO-method

Get the dataframes (name/id/annotationID) attached to an OME object
availableDataframes

Get the dataframes (name/id/annotationID) attached to an OME object
deleteFile,OMERO-method

Delete a file attachend to an OME object
deleteFile

Delete a file attached to an OME object
getAnnotations

Get annotations attached to an OME object. Type, Namespace, Name, Content, ID, FileID (in case of file annotations)
getAnnotations,OMERO-method

Get annotations attached to an OME object. Type, Namespace, Name, Content, ID, FileID (in case of file annotations)
getChannelNames,Image-method

Get the channel names of an Image
getAnnotations,OMEROServer-method

Get annotations attached to an OME object. Type, Namespace, Name, Content, ID, FileID (in case of file annotations)
loadDataframe

Load a dataframe attached to an OME object
attachDataframe

Attaches a dataframe to an OME object
getImages,Dataset-method

Get all images of a dataset
delete,OMERO-method

Deletes an OME object
connect

Connect to an OMERO server
connect,OMEROServer-method

Connect to an OMERO server
getChannelNames

Get the channel names of an Image
disconnect,OMEROServer-method

Disconnect from an OMERO server
attachFile

Attach a file to an OME object
disconnect

Disconnect from an OMERO server
describeDataframe,OMERO-method

Describe a dataframe attached to an OME object
getColumn,Well-method

Get the column index of the specific well
getImages,Plate-method

Get all images of a plate
getPlates

Get all plates of the logged in user
getWells,Plate-method

Get the wells of the specific plate
getProjects,OMEROServer-method

Get all projects of the logged in user
searchFor

Search for OMERO objects
searchFor,OMEROServer-method

Search for OMERO objects
getThumbnail

Get the thumbnail for an Image (as JPEG)
getGroupContext,OMEROServer-method

Get the current group context
getGroupContext

Get the current group context
getOMEROID,OMERO-method

Get the ID of the OME object
describeDataframe

Describe a dataframe attached to an OME object
getContext

Get the current SecurityContext
getContext,OMEROServer-method

Get the current SecurityContext
getPlates,OMEROServer-method

Get all plates of the logged in user
getColumn

Get the column index of the specific well
getPlates,Screen-method

Get the plates of the specific screen
delete

Deletes an OME object
getOMEROID

Get the ID of the OME object
getDatasets,OMEROServer-method

Get all datasets of the logged in user
loadCSV,OMEROServer-method

Load a CSV file from the server
getGateway,OMEROServer-method

Get the reference to the Java Gatway
loadCSV

Load a CSV file from the server
getROIs,Image-method

Get the ROIs (Point, Ellipse or Rectangle) of an Image x, y -> Point x, y, rx, ry -> Ellipse x, y, w, h -> Rectangle theta: Rotation about theta text: An optional comment
getProjects

Get all projects of the logged in user
getGateway

Get the reference to the Java Gatway
getDatasets,Project-method

Get all datasets of a project
getDatasets

Get all datasets of the logged in user
setGroupContext,OMEROServer-method

Set a different group context
getImages,Well-method

Get the fields of the specific well
getRow

Get the row index of the specific well
setGroupContext

Set a different group context
getPixelValues,Image-method

Get the pixel values of an Image. An error will be thrown if invalid z, t or c values are specified.
getImages

Get all images of a container (Dataset, Project, Screen, Plate or Well)
getScreens,OMEROServer-method

Get all screens of the logged in user
getWells

Get the wells of the specific plate
length,Well-method

Get the number of fields
getPixelValues

Get the pixel values of an Image. An error will be thrown if invalid z, t or c values are specified.
getROIs

Get the ROIs (Point, Ellipse or Rectangle) of an Image x, y -> Point x, y, rx, ry -> Ellipse x, y, w, h -> Rectangle theta: Rotation about theta text: An optional comment
getRow,Well-method

Get the row index of the specific well
loadObject,OMEROServer-method

Load an object from the server
loadObject

Load an object from the server
addROIs,Image-method

Add ROIs (Point, Ellipse or Rectangle) to an Image x, y -> Point x, y, rx, ry -> Ellipse x, y, w, h -> Rectangle theta: Rotation about theta text: An optional comment
addROIs

Add ROIs (Point, Ellipse or Rectangle) to an Image x, y -> Point x, y, rx, ry -> Ellipse x, y, w, h -> Rectangle theta: Rotation about theta text: An optional comment
OMERO-class

OME remote object class This is basically a wrapper around the Pojo's of the Java Gateway with a reference to the server.
OMEROServer-class

OMEROServer class Provides access to an OMERO server
Screen-class

Screen
Plate-class

Plate
Project-class

Project
Well-class

Well
Dataset-class

Dataset