= USERs = Please contact [[mailto:claire.stoffel@epfl.ch | Claire Stoffel]] for any question related to OMERO or to the pilot project. = EPFL OMERO server = The EPFL OMERO Public server can be accessed at [[ https://omero.epfl.ch/ | https://omero.epfl.ch/]]. WARNING: To login, hit the `login` button on the top-right corner, and connect with your gaspar credentials. {F16653775} {F16653820} = Breaking news! = (IMPORTANT) **STORAGE SPACE: ** Each participant of the pilot can now use up to 2TB of the storage space! (IMPORTANT) **PUBLIC SHARES: ** It is now fully possible to share images with people outside EPFL: Please go to [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/pilote/publish-data/ | this page ]] to know how to publish data using OMERO.web (NOTE) **OMERO.insight at the BIOP: ** Here is the list of BIOP microscopes that have the OMERO.insight client installed | Zeiss LSM 710| |Visitron SD-W1| |Leica SP8 FLIM| |Leica SP8 STED 3X| |Leica SP8 UP1| |Leica SP8 UP2| |Leica SP8 INV1| |Leica DM5500| |Nikon SIM/STORM| |Zeiss Lightsheet Z1| |Nikon CSU-W1| |Olympus Slide Scanner 1| |Olympus Slide Scanner 2| = Training slides = The slides from the first training session (OMERO introduction) can be accessed [[https://docs.google.com/presentation/d/11RAzRpONymEYehHdVCedFzRB8qbo3QRRm1gJs-Xg0Z8/ | here]]. The slides from the second training session (FIJI and OMERO) can be accessed [[https://docs.google.com/presentation/d/1FUvzQeMTo99tv6gksRoOtMMO78HQY95x2C3whWqN6qE/ | here]]. = OMERO PDF tutorials = You can find here useful pdf tutorials from the OME team: 1. [[ https://downloads.openmicroscopy.org/help/pdfs/importing-data-5.pdf | importing data]] 2. [[ https://downloads.openmicroscopy.org/help/pdfs/managing-data.pdf | managing data]] 3. [[ https://downloads.openmicroscopy.org/help/pdfs/figure.pdf | creating figures]] 4. [[ https://downloads.openmicroscopy.org/help/pdfs/web-tagging.pdf | web-tagging]] 5. [[ https://downloads.openmicroscopy.org/help/pdfs/sharing-data.pdf | sharing data]] 6. [[ https://downloads.openmicroscopy.org/help/pdfs/workflows-fiji.pdf | processing with FIJI]] = Training materials = ===== Demo dataset for the first training session ===== Windows: Go to the path `\\svfas6.epfl.ch\biop\public\0-BIOP_Data\0-Install\OMERO\demo dataset` from your file explorer Mac: Go to the folder `smb://svfas6.epfl.ch/biop/public/0-BIOP_Data/0-Install/OMERO/demo dataset` from the finder ===== Demo dataset for the second training session ===== Windows: Go to the path `\\svfas6.epfl.ch\biop\public\0-BIOP_Data\0-Install\OMERO\demo dataset 2` from your file explorer Mac: Go to the folder `smb://svfas6.epfl.ch/biop/public/0-BIOP_Data/0-Install/OMERO/demo dataset 2` from the finder ===== Additional files for the second training session ===== Windows: Go to the path `\\svfas6.epfl.ch\biop\public\0-BIOP_Data\0-Install\OMERO\demo extra files` from your file explorer Mac: Go to the folder `smb://svfas6.epfl.ch/biop/public/0-BIOP_Data/0-Install/OMERO/demo extra files` from the finder = Hierarchy guidelines for OMERO = - **Project**: Create a new `project` for each of your research projects. Use a short and concise name for the `project`, and add more informations in the form of project tags or in the description section of the project. - **Dataset**: Create a new `dataset` for each individual experiment within a research project. Name the dataset with the date of the experiment. - **Dataset annotations**: Tag the `dataset` with different annotations (tags or key-value pairs) that describe the whole experiment (type of experiment, conditions that apply to the whole dataset..) - **Image annotations**: Tag the `images` in a dataset with the different conditions used for each image

https://wiki-biop.epfl.ch/en/Image_Storage/OMERO/AdminOmeroGeneral https://wiki-biop.epfl.ch/en/Image_Storage/OMERO/Managing_Data https://wiki-biop.epfl.ch/en/Image_Storage/OMERO/Home

= USERs = Please contact [[mailto:claire.stoffel@epfl.ch | Claire Stoffel]] for any question related to OMERO or to the pilot project. = EPFL OMERO server = The EPFL OMERO Public server can be accessed at [[ https://omero.epfl.ch/ | https://omero.epfl.ch/]]. WARNING: To login, hit the `login` button on the top-right corner, and connect with your gaspar credentials. {F16653775} {F16653820} = Breaking news! = (IMPORTANT) **STORAGE SPACE: ** Each participant of the pilot can now use up to 2TB of the storage space! (IMPORTANT) **PUBLIC SHARES: ** It is now fully possible to share images with people outside EPFL: Please go to [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/pilote/publish-data/ | this page ]] to know how to publish data using OMERO.web (NOTE) **OMERO.insight at the BIOP: ** Here is the list of BIOP microscopes that have the OMERO.insight client installed | Zeiss LSM 710| |Visitron SD-W1| |Leica SP8 FLIM| |Leica SP8 STED 3X| |Leica SP8 UP1| |Leica SP8 UP2| |Leica SP8 INV1| |Leica DM5500| |Nikon SIM/STORM| |Zeiss Lightsheet Z1| |Nikon CSU-W1| |Olympus Slide Scanner 1| |Olympus Slide Scanner 2| = Training slides = The slides from the first training session (OMERO introduction) can be accessed [[https://docs.google.com/presentation/d/11RAzRpONymEYehHdVCedFzRB8qbo3QRRm1gJs-Xg0Z8/ | here]]. The slides from the second training session (FIJI and OMERO) can be accessed [[https://docs.google.com/presentation/d/1FUvzQeMTo99tv6gksRoOtMMO78HQY95x2C3whWqN6qE/ | here]]. = OMERO PDF tutorials = You can find here useful pdf tutorials from the OME team: 1. [[ https://downloads.openmicroscopy.org/help/pdfs/importing-data-5.pdf | importing data]] 2. [[ https://downloads.openmicroscopy.org/help/pdfs/managing-data.pdf | managing data]] 3. [[ https://downloads.openmicroscopy.org/help/pdfs/figure.pdf | creating figures]] 4. [[ https://downloads.openmicroscopy.org/help/pdfs/web-tagging.pdf | web-tagging]] 5. [[ https://downloads.openmicroscopy.org/help/pdfs/sharing-data.pdf | sharing data]] 6. [[ https://downloads.openmicroscopy.org/help/pdfs/workflows-fiji.pdf | processing with FIJI]] = Training materials = ===== Demo dataset for the first training session ===== Windows: Go to the path `\\svfas6.epfl.ch\biop\public\0-BIOP_Data\0-Install\OMERO\demo dataset` from your file explorer Mac: Go to the folder `smb://svfas6.epfl.ch/biop/public/0-BIOP_Data/0-Install/OMERO/demo dataset` from the finder ===== Demo dataset for the second training session ===== Windows: Go to the path `\\svfas6.epfl.ch\biop\public\0-BIOP_Data\0-Install\OMERO\demo dataset 2` from your file explorer Mac: Go to the folder `smb://svfas6.epfl.ch/biop/public/0-BIOP_Data/0-Install/OMERO/demo dataset 2` from the finder ===== Additional files for the second training session =====https://wiki-biop.epfl.ch/en/Image_Storage/OMERO/AdminOmeroGeneral Windows: Go to the path `\\svfas6https://wiki-biop.epfl.ch\biop\public\0-BIOP_Data\0-Install\ch/en/Image_Storage/OMERO\demo extra files` from your file explorer/Managing_Data Mac: Go to the folder `smb://svfas6https://wiki-biop.epfl.ch/biop/public/0-BIOP_Data/0-Install/OMERO/demo extra files` from the finder = Hierarchy guidelines for OMERO = - **Project**: Create a new `project` for each of your research projects. Use a short and concise name for the `project`, and add more informations in the form of project tags or in the description section of the project. - **Dataset**: Create a new `dataset` for each individual experiment within a research project. Name the dataset with the date of the experiment. - **Dataset annotations**: Tag the `dataset` with different annotations (tags or key-value pairs) that describe the whole experiment (type of experiment, conditions that apply to the whole dataset..) - **Image annotations**: Tag the `images` in a dataset with the different conditions used for each image en/Image_Storage/OMERO/Home