= Data management in OMERO.web = == Manage Images in Datasets/Projects == # **Organize your data** in the left-hand side tree by creating new Projects and Datasets. You can link the Images to the new or existing Datasets and Datasets to new or existing Projects. For HCS data, you can create new Screens and link Plates to these Screens. # **Move your data**: Drag and drop Images between Datasets and Datasets between Projects. For HCS data, drag and drop Plates between Screens. # **Copy Images**: using the right-click context menu: -- Select the Images (resp. Dataset) to be copied, then right-click and click {nav Edit > Copy Link}. -- Select the Dataset (resp. Project) you want to copy the Images (resp. Dataset) to, right-click and click on {nav Edit > Paste Link}. {F18235014, layout=inline, width=300} {F18235018, layout=inline, width=300} WARNING: The **Copy Link** feature will only create new links between an Image and a Dataset, so that one Image becomes linked to multiple Datasets. **This does not create a new independent copy of the Image**. The only ways to create a fully independent copy in OMERO is to use the [[ https://omero-guides.readthedocs.io/en/latest/introduction/docs/data-management.html#duplicatecli | Duplicate feature (CLI) ]] or to re-import the file. If you delete one of the Datasets, any Images within it that are linked to other Datasets will be retained. Nevertheless,** if you directly select and delete an Image that has been copied from another Dataset it will be deleted and lost from both Datasets**. There is a clear warning in the OMERO.web when you try to delete such a doubly linked Image, see screenshot below: {F18234860, size=full} == Move data between groups == Users can be a member and have their data in one or more Groups. Thus it is sometimes necessary to move the data between groups. If you are an owner of the data, you can move the data between the groups you are a member of. NOTE: Caution has to be taken in case the data are linked to other users’ containers (Datasets, Projects). If you move only the contents of those containers (Datasets or Images) and not the containers themselves (Projects or Datasets), the links between such containers and the Images or Datasets which are moved will be deleted. Further, if any objects are moved, the links to any annotations such as Tags or attached File annotations linked to these objects will be deleted in case these annotations belong to others or in case these annotations belong to you but** are also linked to some other objects in the original group** which are not being moved. # In OMERO.web, select the data to be moved in the left-hand side tree. # Right-click and select {nav Move to Group....} # Select the group you want to move the data to. # A message {nav Checking which linked objects will be moved} will appear and a spinner to the left of it. Wait until the spinner vanishes and a list of objects to be moved and a list of objects which are not included in the move appears. # Check both lists. Please read the note above about which objects are typically not included and reconsider the Move action. The not included objects will not be linked to the Moved objects anymore if you go ahead with the move, the linkage will be lost. # In case you are happy with the {nav Move} action, select a target Dataset or Project or create a new one and click {nav OK}. {F18235225,layout=inline, height=300}{F18235288,layout=inline, height=300} == Change ownership of data (for PIs) == Every object in OMERO has a single, particular user as an owner. The ownership of objects can be changed but only if you are an Administrator, Administrator with restricted privileges or a Group owner. If you are a PI but are not the Group owner of your lab's OMERO group, please contact [[mailto:claire.stoffel@epfl.ch | Claire Stoffel]]. # Select a Project, Dataset or Images in the left-hand side tree of OMERO.web. # Right-click and in the context menu, select {nav Change owner}. # In the new dialog, select the new owner of the data. # Wait until the {nav Checking which objects will be moved} is done and the spinner vanishes. {F18235112, float, layout=right, width=360} This might take time depending on the number of objects you are attempting to change owner of. For example, a large number of ROIs on the images can be a cause of longer waiting times. # Pick the new owner and check the list of objects which are supposed to be transferred to the new owner. Also consider the possible loss of linkage between objects listed in the {nav Will be removed from} line. Click {nav OK}. {F18235158, width=300} = More documentation on this topic... = To learn more about annotating OMERO images, we recommend you to visit the [[ https://omero-guides.readthedocs.io/en/latest/introduction/docs/data-management.html | dedicated page from the official OMERO guide ]]. --- {icon hand-o-right} [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/figures/ | NEXT STEP: Creating Figures ]] ---

= Data management in OMERO.web = == Manage Images in Datasets/Projects == # **Organize your data** in the left-hand side tree by creating new Projects and Datasets. You can link the Images to the new or existing Datasets and Datasets to new or existing Projects. For HCS data, you can create new Screens and link Plates to these Screens. # **Move your data**: Drag and drop Images between Datasets and Datasets between Projects. For HCS data, drag and drop Plates between Screens. # **Copy Images**: using the right-click context menu: -- Select the Images (resp. Dataset) to be copied, then right-click and click {nav Edit > Copy Link}. -- Select the Dataset (resp. Project) you want to copy the Images (resp. Dataset) to, right-click and click on {nav Edit > Paste Link}. {F18235014, layout=inline, width=300} {F18235018, layout=inline, width=300} WARNING: The **Copy Link** feature will only create new links between an Image and a Dataset, so that one Image becomes linked to multiple Datasets. **This does not create a new independent copy of the Image**. The only ways to create a fully independent copy in OMERO is to use the [[ https://omero-guides.readthedocs.io/en/latest/introduction/docs/data-management.html#duplicatecli | Duplicate feature (CLI) ]] or to re-import the file. If you delete one of the Datasets, any Images within it that are linked to other Datasets will be retained. Nevertheless,** if you directly select and delete an Image that has been copied from another Dataset it will be deleted and lost from both Datasets**. There is a clear warning in the OMERO.web when you try to delete such a doubly linked Image, see screenshot below: {F18234860, size=full} == Move data between groups == Users can be a member and have their data in one or more Groups. Thus it is sometimes necessary to move the data between groups. If you are an owner of the data, you can move the data between the groups you are a member of. NOTE: Caution has to be taken in case the data are linked to other users’ containers (Datasets, Projects). If you move only the contents of those containers (Datasets or Images) and not the containers themselves (Projects or Datasets), the links between such containers and the Images or Datasets which are moved will be deleted. Further, if any objects are moved, the links to any annotations such as Tags or attached File annotations linked to these objects will be deleted in case these annotations belong to others or in case these annotations belong to you but** are also linked to some other objects in the original group** which are not being moved. # In OMERO.web, select the data to be moved in the left-hand side tree. # Right-click and select {nav Move to Group....} # Select the group you want to move the data to. # A message {nav Checking which linked objects will be moved} will appear and a spinner to the left of it. Wait until the spinner vanishes and a list of objects to be moved and a list of objects which are not included in the move appears. # Check both lists. Please read the note above about which objects are typically not included and reconsider the Move action. The not included objects will not be linked to the Moved objects anymore if you go ahead with the move, the linkage will be lost. # In case you are happy with the {nav Move} action, select a target Dataset or Project or create a new one and click {nav OK}. {F18235225,layout=inline, height=300}{F18235288,layout=inline, height=300} == Change ownership of data (for group owners) == Every object in OMERO has a single, particular user as an owner. The ownership of objects can be changed but only if you are an Administrator, Administrator with restricted privileges or a Group owner. If you are a PI but are not the Group owner of your lab's OMERO group, please contact [[mailto:claire.stoffel@epfl.ch | Claire Stoffel]]. # Select a Project, Dataset or Images in the left-hand side tree of OMERO.web. # Right-click and in the context menu, select {nav Change owner}. # In the new dialog, select the new owner of the data. # Wait until the {nav Checking which objects will be moved} is done and the spinner vanishes. {F18235112, float, layout=right, width=360} This might take time depending on the number of objects you are attempting to change owner of. For example, a large number of ROIs on the images can be a cause of longer waiting times. # Pick the new owner and check the list of objects which are supposed to be transferred to the new owner. Also consider the possible loss of linkage between objects listed in the {nav Will be removed from} line. Click {nav OK}. {F18235158, width=300} = More documentation on this topic... = To learn more about annotating OMERO images, we recommend you to visit the [[ https://omero-guides.readthedocs.io/en/latest/introduction/docs/data-management.html | dedicated page from the official OMERO guide ]]. --- {icon hand-o-right} [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/figures/ | NEXT STEP: Creating Figures ]] ---

= Data management in OMERO.web = == Manage Images in Datasets/Projects == # **Organize your data** in the left-hand side tree by creating new Projects and Datasets. You can link the Images to the new or existing Datasets and Datasets to new or existing Projects. For HCS data, you can create new Screens and link Plates to these Screens. # **Move your data**: Drag and drop Images between Datasets and Datasets between Projects. For HCS data, drag and drop Plates between Screens. # **Copy Images**: using the right-click context menu: -- Select the Images (resp. Dataset) to be copied, then right-click and click {nav Edit > Copy Link}. -- Select the Dataset (resp. Project) you want to copy the Images (resp. Dataset) to, right-click and click on {nav Edit > Paste Link}. {F18235014, layout=inline, width=300} {F18235018, layout=inline, width=300} WARNING: The **Copy Link** feature will only create new links between an Image and a Dataset, so that one Image becomes linked to multiple Datasets. **This does not create a new independent copy of the Image**. The only ways to create a fully independent copy in OMERO is to use the [[ https://omero-guides.readthedocs.io/en/latest/introduction/docs/data-management.html#duplicatecli | Duplicate feature (CLI) ]] or to re-import the file. If you delete one of the Datasets, any Images within it that are linked to other Datasets will be retained. Nevertheless,** if you directly select and delete an Image that has been copied from another Dataset it will be deleted and lost from both Datasets**. There is a clear warning in the OMERO.web when you try to delete such a doubly linked Image, see screenshot below: {F18234860, size=full} == Move data between groups == Users can be a member and have their data in one or more Groups. Thus it is sometimes necessary to move the data between groups. If you are an owner of the data, you can move the data between the groups you are a member of. NOTE: Caution has to be taken in case the data are linked to other users’ containers (Datasets, Projects). If you move only the contents of those containers (Datasets or Images) and not the containers themselves (Projects or Datasets), the links between such containers and the Images or Datasets which are moved will be deleted. Further, if any objects are moved, the links to any annotations such as Tags or attached File annotations linked to these objects will be deleted in case these annotations belong to others or in case these annotations belong to you but** are also linked to some other objects in the original group** which are not being moved. # In OMERO.web, select the data to be moved in the left-hand side tree. # Right-click and select {nav Move to Group....} # Select the group you want to move the data to. # A message {nav Checking which linked objects will be moved} will appear and a spinner to the left of it. Wait until the spinner vanishes and a list of objects to be moved and a list of objects which are not included in the move appears. # Check both lists. Please read the note above about which objects are typically not included and reconsider the Move action. The not included objects will not be linked to the Moved objects anymore if you go ahead with the move, the linkage will be lost. # In case you are happy with the {nav Move} action, select a target Dataset or Project or create a new one and click {nav OK}. {F18235225,layout=inline, height=300}{F18235288,layout=inline, height=300} == Change ownership of data (for PIgroup owners) == Every object in OMERO has a single, particular user as an owner. The ownership of objects can be changed but only if you are an Administrator, Administrator with restricted privileges or a Group owner. If you are a PI but are not the Group owner of your lab's OMERO group, please contact [[mailto:claire.stoffel@epfl.ch | Claire Stoffel]]. # Select a Project, Dataset or Images in the left-hand side tree of OMERO.web. # Right-click and in the context menu, select {nav Change owner}. # In the new dialog, select the new owner of the data. # Wait until the {nav Checking which objects will be moved} is done and the spinner vanishes. {F18235112, float, layout=right, width=360} This might take time depending on the number of objects you are attempting to change owner of. For example, a large number of ROIs on the images can be a cause of longer waiting times. # Pick the new owner and check the list of objects which are supposed to be transferred to the new owner. Also consider the possible loss of linkage between objects listed in the {nav Will be removed from} line. Click {nav OK}. {F18235158, width=300} = More documentation on this topic... = To learn more about annotating OMERO images, we recommend you to visit the [[ https://omero-guides.readthedocs.io/en/latest/introduction/docs/data-management.html | dedicated page from the official OMERO guide ]]. --- {icon hand-o-right} [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/figures/ | NEXT STEP: Creating Figures ]] ---