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= Installing and using romero.gateway package in RStudio = == Windows == This example uses Windows 10, other Windows version should be similar. - Install a JDK, for example [[ https://adoptopenjdk.net/ | AdoptOpenJDK ]]. Make sure to tick the checkbox to set the JAVA_HOME and PATH environment variables during the installation. - In Rstudio, go to `Tools` > `Install Packages...` - Install the dependencies `httr`, `jpeg` and `rJava` from CRAN: {F17572511} - Download the latest `romero.gateway` release zip from [[ https://github.com/ome/rOMERO-gateway/releases | Github ]] and install it: {F17572524} = Analyze OMERO data using R = Load the library: ``` library(romero.gateway) ``` Connect to OMERO (Replace USERNAME and PASSWORD with your gaspar credentials) ``` server <- OMEROServer(host = 'omero.epfl.ch', port = 4064, username=USERNAME, password=PASSWORD) server <- connect(server) paste('Successfully logged in as', server@user$getUserName()) ``` You can see examples on how to analyze OMERO data with R in this [[ https://mybinder.org/v2/gh/ome/omero-guide-r/master?filepath=notebooks/idr0021_Segmentation.ipynb | jupyter notebook ]]: This notebook uses the EBImage package. If you don't have it, you can download it from [[https://bioconductor.org/packages/release/bioc/html/EBImage.html | here ]].

= Installing and using romero.gateway package in RStudio = == Windows == This example uses Windows 10, other Windows version should be similar. - Install a JDK, for example [[ https://adoptopenjdk.net/ | AdoptOpenJDK ]]. Make sure to tick the checkbox to set the JAVA_HOME and PATH environment variables during the installation. - In Rstudio, go to `Tools` > `Install Packages...` - Install the dependencies `httr`, `jpeg` and `rJava` from CRAN: {F17572511} - Download the latest `romero.gateway` release zip from [[ https://github.com/ome/rOMERO-gateway/releases | Github ]] and install it: {F17572524} = Analyze OMERO data using R = Load the library: ``` library(romero.gateway) ``` Connect to OMERO (Enter your gaspar credentials) ``` user_name = readline('Username: ') user_password = readline('Password: ') server <- OMEROServer(host = 'omero.epfl.ch', port = 4064, username=user_name, password=user_password) server <- connect(server) paste('Successfully logged in as', server@user$getUserName()) ``` You can see examples on how to analyze OMERO data with R in this [[ https://mybinder.org/v2/gh/ome/omero-guide-r/master?filepath=notebooks/idr0021_Segmentation.ipynb | jupyter notebook ]]: This notebook uses the EBImage package. If you don't have it, you can download it from [[https://bioconductor.org/packages/release/bioc/html/EBImage.html | here ]].

= Installing and using romero.gateway package in RStudio = == Windows == This example uses Windows 10, other Windows version should be similar. - Install a JDK, for example [[ https://adoptopenjdk.net/ | AdoptOpenJDK ]]. Make sure to tick the checkbox to set the JAVA_HOME and PATH environment variables during the installation. - In Rstudio, go to `Tools` > `Install Packages...` - Install the dependencies `httr`, `jpeg` and `rJava` from CRAN: {F17572511} - Download the latest `romero.gateway` release zip from [[ https://github.com/ome/rOMERO-gateway/releases | Github ]] and install it: {F17572524} = Analyze OMERO data using R = Load the library: ``` library(romero.gateway) ``` Connect to OMERO (Replace USERNAME and PASSWORD withEnter your gaspar credentials) ``` user_name = readline('Username: ') user_password = readline('Password: ') server <- OMEROServer(host = 'omero.epfl.ch', port = 4064, username=USERNAMEuser_name, password=PASSWORDuser_password) server <- connect(server) paste('Successfully logged in as', server@user$getUserName()) ``` You can see examples on how to analyze OMERO data with R in this [[ https://mybinder.org/v2/gh/ome/omero-guide-r/master?filepath=notebooks/idr0021_Segmentation.ipynb | jupyter notebook ]]: This notebook uses the EBImage package. If you don't have it, you can download it from [[https://bioconductor.org/packages/release/bioc/html/EBImage.html | here ]].