= 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
|CF05 - Zeiss LSM 710|
|CF10 - Visitron CSU-W1|
|CF13 - Leica SP8 FLIM|
|CF14 - Leica SP8 STED 3X|
|CF15 - Leica SP8 Upright I|
|CF16 - Leica SP8 Upright II|
|CF17 - Leica SP8 Inverted I|
|CF18 - Nikon CSU-W1|
|WF01 - Leica DM5500|
|WF09 - Nikon SIM/STORM|
|WF12 - ZEISS Lightsheet Z1|
|WF10 - Olympus Slide Scanner 1|
|WF13 - Olympus Slide Scanner 2|
|WF15 - Operetta CLS|
= 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