Phriction Projects Wikis Bioimaging And Optics Platform Image Processing OMERO Viewing Data History Version 2 vs 3
Version 2 vs 3
Version 2 vs 3
Content Changes
Content Changes
= Viewing Data from the web using the OMERO.iviewer web app =
===** Open an image in the OMERO.iviewer **===
OMERO.iviewer is a Web app that can be accessed from the [[ https://omero.epfl.ch/webclient/ | EPFL-OMERO webclient (OMERO.web) ]].
From OMERO.web, double-click on an Image thumbnail to open an Image in OMERO.iviewer.
This can also be done by hitting the {nav Full Viewer} button under the {nav Preview} tab from the right-hand pane, or with a right-clic on an image name from the left-hand tree and selecting {nav Open with... > OMERO.iviewer}.
{F19856865}
{F19856818}
===** OMERO.iviewer: the basics **===
{F19856779, size = full}
===** Synchronize multiple viewer windows **===
{F19856781, size = full}
===** Edit and save the rendering settings **===
{F19856783, size = full}
===** Work with Regions of Interest in the iviewer **===
{F19856785, size = full}
= More documentation on this topic... =
To learn in more details (with step-by-step explanations) how to...
- open multidimensional images in OMERO.iviewer
- change rendering settings in OMERO.iviewer and scroll through z and t
- change the Lookup table and invert the displayed intensities for a particular channel
- use the Histogram feature
- zoom and rotate the image
- create a maximum intensity Projection and save it
- save a current viewport as png in OMERO.iviewer
- use and synchronize multiple viewer windows inside OMERO.iviewer
- work with ROIs in OMERO.iviewer
we recommend you to visit the [[ https://omero-guides.readthedocs.io/en/latest/iviewer/docs/index.html | dedicated page from the official OMERO guide ]].
= Viewing High Content Screening (HCS) Data =
OMERO allows the importing, storing and viewing of screening data. Many common formats (like the .xml and .tiff files generated by the PerkinElmer Operetta available at the BIOP) are supported and benefit from a plate and field view in OMERO.web:
{F19856952, size=full}
(IMPORTANT) Please look at the //[[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/data-upload/file-formats/ | How to import to OMERO depending on the file-format ]]// guide to learn how to upload HCS data to OMERO.
In OMERO.web, screens are represented in the data tree by dark grey folders.
Expand the Screen folder, expand the Plate container and select a Run.
Click on a well in the plate shown on the centre pane to view the data in that well.
Double-click on a well to open the image in the full viewer.
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{icon hand-o-right} [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/annotating-data/ | NEXT STEP: Annotating data ]]
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https://wiki-biop.epfl.ch/en/Image_Storage/OMERO/Viewing_Data
= Viewing Data from the web using the OMERO.iviewer web app =
===** Open an image in the OMERO.iviewer **===
OMERO.iviewer is a Web app that can be accessed from the [[ https://omero.epfl.ch/webclient/ | EPFL-OMERO webclient (OMERO.web) ]].
From OMERO.web, double-click on an Image thumbnail to open an Image in OMERO.iviewer.
This can also be done by hitting the {nav Full Viewer} button under the {nav Preview} tab from the right-hand pane, or with a right-clic on an image name from the left-hand tree and selecting {nav Open with... > OMERO.iviewer}.
{F19856865}
{F19856818}
===** OMERO.iviewer: the basics **===
{F19856779, size = full}
===** Synchronize multiple viewer windows **===
{F19856781, size = full}
===** Edit and save the rendering settings **===
{F19856783, size = full}
===** Work with Regions of Interest in the iviewer **===
{F19856785, size = full}
= More documentation on this topic... =
To learn in more details (with step-by-step explanations) how to...
- open multidimensional images in OMERO.iviewer
- change rendering settings in OMERO.iviewer and scroll through z and t
- change the Lookup table and invert the displayed intensities for a particular channel
- use the Histogram feature
- zoom and rotate the image
- create a maximum intensity Projection and save it
- save a current viewport as png in OMERO.iviewer
- use and synchronize multiple viewer windows inside OMERO.iviewer
- work with ROIs in OMERO.iviewer
we recommend you to visit the [[ https://omero-guides.readthedocs.io/en/latest/iviewer/docs/index.html | dedicated page from the official OMERO guide ]].
= Viewing High Content Screening (HCS) Data =
OMERO allows the importing, storing and viewing of screening data. Many common formats (like the .xml and .tiff files generated by the PerkinElmer Operetta available at the BIOP) are supported and benefit from a plate and field view in OMERO.web:
{F19856952, size=full}
(IMPORTANT) Please look at the //[[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/data-upload/file-formats/ | How to import to OMERO depending on the file-format ]]// guide to learn how to upload HCS data to OMERO.
In OMERO.web, screens are represented in the data tree by dark grey folders.
Expand the Screen folder, expand the Plate container and select a Run.
Click on a well in the plate shown on the centre pane to view the data in that well.
Double-click on a well to open the image in the full viewer.
---
{icon hand-o-right} [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/annotating-data/ | NEXT STEP: Annotating data ]]
---
https://wiki-biop.epfl.ch/en/Image_Storage/OMERO/Viewing_Data
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