Phriction Projects Wikis Bioimaging And Optics Platform Image Processing OMERO OMERO Pilot History Version 27 vs 28
Version 27 vs 28
Version 27 vs 28
Content Changes
Content Changes
= USERs =
Please contact [[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
= 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
= 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
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