Examples of Customized Imports
12. Make sure that the Create workspace folder from search string check box is selected while the other is cleared
13. Click OK to load the scenes Image A and Image B to the workspace. Examine the executed import in the Workspace window and open the created scenes. If not all image layers are displayed, check the Image Layer Mixing.
Figure 51: Imported sample scene.
If you are not satisfied with the import, reopen the Customized Import dialog box and go back to step 5.
Alternatively, you can load the sample import template to the Customized Import dialog box. Click the Load button and select the import template file named Usecase 1.xml. The path is C:\Program Files\Definiens
Developer Version number\Examples
\CustomizedImport\Usecase 1.xml.
Be sure to select the Root Folder (see step 6)and Sample File (see step 7) before you click OK.
(ellipsis button)
Edit the Image Layer Mixing on page 97
Use Case 2: Single Layer Complex
Each scene consists of three image layer .tif files each stored in a different folder.
Figure 52: Use case 2: Folder structure (left) with file contained in the highlighted folder (right).
4. Click the Clear button before configuring a new import.
5. If there are scenes in the workspace, click the Clear Workspace button to remove them.
6. Select the Root Folder named root folder usecase 2. The default path is C:\Program Files\Definiens Developer Version number\Examples
\CustomizedImport\root folder usecase 2. The Root Folder text box displays this path.
7. Select a Master File, for example Layer1.tif within the subfolder layer folder 1.
While the Sample File text box displays the path below the root folder (image A\layer folder 1\Layer1.tif), the Search String text box displays
{{root}\{any-folders}\{scene}.tif:reverse}.
8. Press the Test button to preview the naming result of the Master File based on the Search String.
9. The Preview is not correct because the scene is found as Layer1 instead of image_A. To define the scene name and all static parts of the search string, you have to edit the Search String as follows:
{{root}\{scene}\layer folder 1\Layer1.tif:reverse}.
10. After the master file is defined, the scene needs to be set up. To do so, go to the Image Layers tab. Under File 1 the settings of a master file are already predefined.
Change here the search string to:
For Layer 1 use {{root}\{scene}\layer folder 1\Layer1.tif:reverse}.
For Layer 2 use {{root}\{scene}\layer folder 2\Layer2.tif:reverse}.
For Layer 3 use {{root}\{scene}\layer folder 3\Layer3.tif:reverse}.
Type Layer 1 as Alias.
To define Layer2, click the Add File button to open the Import Image Layer dialog box. Navigate to Image_A_Layer2.tif and open it. Under File 2 type Layer 2 as Alias.
For Layer 3 proceed accordingly.
11. Make sure that the Create workspace folder from search string check box is selected while the other is cleared.
12. Click OK to load the scenes Image A and Image B to the workspace. Examine the executed import in the Workspace window and open the created scenes. If not all image layers are displayed, check the Image Layer Mixing.
Figure 53: Imported sample scene.
(ellipsis button)
Edit the Image Layer Mixing on page 97
If you are not satisfied with the import, reopen the Customized Import dialog box and go back to step 5.
Alternatively, you can load the sample import template to the Customized Import dialog box. Click the Load button and select the import template file named Usecase 2.xml. The path is C:\Program Files\Definiens
Developer Version number\Examples
\CustomizedImport\Usecase 2.xml.
Be sure to select the Root Folder (see step 6)and Master File (see step 7) before you click OK.
Use Case 3: Multi-Layer and Layer Alias
Each scene consists of two .tif files: one with three image layers, one with a single layer both stored in one folder.
Figure 54: Use case 3: Folder structure (left) with file contained in the highlighted folder (right).
4. Click the Clear button before configuring a new import.
5. If there are scenes in the workspace, click the Clear Workspace button to remove them.
6. Select the Root Folder named root folder usecase 3. The default path is C:\Program Files\Definiens Developer Version number\Examples
\CustomizedImport\root folder usecase 3. The Root Folder text box displays this path.
7. Select a Master File, for example imageA_multilayer.tif within the subfolder image A. While the Sample File text box displays the path below the root folder (image A\imageA_multilayer.tif), the Search String text box displays
{{root}\{any-folders}\{scene}.tif:reverse}.
8. Press the Test button to preview the naming result of the Master File based on the Search String.
9. The Preview is not yet satisfying because the scene is found as imageA_multilayer instead of Image A. You have to edit the Search String as follows:
{{root}\{any-folders}\{scene}_multilayer.tif:reverse}
10. After the master file is defined, the scene needs to be set up. To do so, go to the Image Layers tab. Under File 1 the settings of a master file are already predefined.
11. a.) If no image layer aliases are used set the layer properties as follows:
Add to the predefined File 1 another File 2 by clicking the Add File button. For File 2 change the search string as follows:
• For Layer 1 use {{root}\{any-folders}\{scene}_multilayer.tif:reverse}.
• For Layer 2 use {{root}\{any-folders}\{scene}_single layer.tif:reverse}.
b.) If you want to use image layer aliases, set the layer properties as follows:
Add to the predefined File 1 another File 2 by clicking the Add File button. For File 2 change the search string as follows:
• For Layer 1 use {{root}\{any-folders}\{scene}_multilayer.tif:reverse}.
Define the layer alias as alias1.
Set the Channel index to 1, defining that the first channel of this file is loaded.
• For Layer 2 use {{root}\{any-folders}\{scene}_multilayer.tif:reverse}.
Define the layer alias as alias2.
Set the Channel index to 2, defining that the second channel of this file is loaded.
• For Layer 3 use {{root}\{any-folders}\{scene}_multilayer.tif:reverse}.
Define the layer alias as alias3.
Set the Channel index to 3, defining that the third channel of this file is loaded.
• For Layer 4 use {{root}\{any-folders}\{scene}_singlelayer.tif:reverse}.
Define the layer alias as alias4.
Since this is a one layer file, you do not need to edit the channel index.
Further change under the File 1 group, the following Alias entries:
• For the Alias of Layer 1 type alias1.
• For the Alias of Layer 2 type alias2.
• For the Alias of Layer 3 type alias3.
Under the File 2 group, change the following Alias entries:
• For the Alias of Layer 1 type alias4.
12. Make sure that the Create workspace folder from search string check box is selected while the other is cleared.
13. Click OK to load the scenes Image A and Image B to the workspace. Check the executed import in the Workspace window and open the created scenes. Check the Image Layer Mixing to see if Layer 4 is loaded as well. If not, you can select colors for Layer 4, for example, R and G.
Figure 55: Imported sample scene of Use Case 3.
Figure 56: Sample setting in the Edit Image Layer Mixing dialog box for displaying all image layers.
If you are not satisfied with the import, reopen the Customized Import dialog box and go back to step 5.
Alternatively, you can load the sample import template to the Customized Import dialog box. Click the Load button and select the import template file named Usecase 3 no alias.xml or Usecase 3 with alias.xml. the path is
Edit the Image Layer Mixing on page 97
C:\Program Files\Definiens Developer Version number\Examples
\CustomizedImport\
Be sure to select the Root Folder (see step 6)and Sample File (see step 7) before you click OK.
5.2.4 Change the View in the Workspace
The Workspace window provides different views of projects.
You can switch among the following:
• List View
• Folder View
• Small Thumbnails
• Large Thumbnails
You can also filter the columns displayed in the List View and the Folder View.
To switch views, click the drop-down arrow at bottom of the right pane of the Workspace window and select one of the options.
List View
In the List View, the right pane of the Workspace window lists all projects contained in the selected structure hierarchy of the tree view. This includes also projects contained in sub-structures. The position of a project within the structure is noted in the project name: Each path level is separated by a period. With the List View you have direct access to all projects in your workspace.
Figure 57: Workspace window with activated List View.
Folder View
In the Folder View, you only see the content of the selected structure, either folders or projects. Double-click a folder to see its contents. The Folder View displays structural elements to help you navigate.
Figure 58: Workspace window with activated Folder View. (Image data courtesy of BioImage A/S).
Thumbnail View
Using the Small or Large Thumbnails, you can select any folder to see thumbnails of the contents. Double-click any thumbnail to open it in the project view. The open image is marked in the Thumbnail view with an asterisk (*) before the file name.
Figure 59: Large Thumbnails view in the Workspace window. (Image data courtesy of BioImage A/S).
To change the display of the thumbnails, select Thumbnail Settings in the context menu or go to the main menu bar and select View > Thumbnail Settings.
Set Filters for the Workspace
Click the Filters button to open the Filter Settings window and create filters for the projects in the right pane of the workspace.
Figure 60: Filter Settings dialog box.
Edit Image Layer Mixing for Thumbnails on page 98
1. To create a filter, select the category you want to filter in the Filter column and type in the text for the projects you want to view. Click OK.
The right pane displays a colored background and your filter excludes all data that does not include the text of your filter.
2. To remove a filter, select it in the Filter column and click the Clear Filter button.
5.2.5 Manage Folders in the Workspace Tree View
Add, move, and rename folders in the tree view on the left pane of the Workspace window. Depending on the import template, these folders may represent different items, such as Assay, Well, Plate or Run for a cell screening device.
1. To add an item, right-click a folder and select Add [Item].
2. The new folder is displayed in the tree view of the Workspace window. You can edit the folder name. To rename a folder, right-click it and choose Rename on the context menu.
3. Move folders to rearrange them by drag-and-drop operations.
5.2.6 Save a Workspace
Save the currently open workspace to a .dpj file.
To save a workspace, do one of the following:
• Choose File > Save Workspace on the main menu bar.
• Choose File > Save Workspace As on the main menu bar. The Save Workspace dialog box opens. Select a folder and enter a name for the workspace file (.dpj).
Click the Save button to store the file.
5.2.7 Close a Workspace
Close the currently open workspace.
1. To close a currently open workspace, do one of the following:
• Choose File > Close Workspace on the main menu bar.
• If available, create a new workspace.
• Open an existing workspace.
2. If the workspace has changed, you are asked to save the modifications. Select Yes for saving and closing. Select No to close the workspace without saving.
Save Workspace
Create a New Workspace on page 58
Open an Existing Workspace on page 84
5.2.8 Move a Workspace
Moving a workspace is easy because you can move the complete workspace folder and continue working with the workspace on the new location.
If file connections related to the input data are lost, the Locate Image dialog box opens.
Browse to the new location and reconnect the image. This automatically updates all other input data files which are stored under the same input root folder. If you have loaded input data from multiple input root folders, you only have to relocate one file per input root folder to update all file connections.
Use the same procedure if input data has been moved.
We recommend that you not move any output files which are stored by default within the workspace folder. These are typically all .dpr project files and by default, all result files. However, if you do, you can modify the path of the output root folder under which all output files are stored.
1. To modify the path of the output root folder choose File > Workspace Properties on the main menu bar. The Workspace Properties dialog box opens.
Figure 61: Workspace Properties dialog box.
2. Clear the Use workspace folder check box and change the path of the output root folder by editing it. Alternatively, you can click the ellipsis button and browse to an output root folder.
5.2.9 Open an Existing Workspace
Open an existing workspace from a file.
1. To open an existing workspace, do one of the following:
• Click the Open Workspace button on the File toolbar.
• Choose File > Open Workspace on the main menu bar.
The Open Workspace dialog box opens.
2. Browse for an Definiens workspace file (.dpj).
3. Click Open. The folder tree of the workspace is displayed in the left pane (the tree view) of the Workspace window.
5.2.10 View a Project
Open a project to view and investigate it in the project view.
1. Go to the right pane of the Workspace window that lists all projects of a workspace.
Create a New Workspace on page 58
(ellipsis button)
Open Workspace
2. To view a project, do one of the following:
• Right-click a project and choose Open on the context menu.
• Double-click a project.
• Select a project and press Enter.
3. The project opens and is displayed in the project view. If another project is already open, it is closed before opening the other one.
For more information about opening and viewing projects, see the related instructional chapters.
Open a Subset Only
If scenes are very large, you can open and investigate a subset of the project.
1. Go to the right pane of the Workspace window that lists all projects of a workspace.
2. Right-click a project and choose Open Subset. The Subset Selection dialog box opens.
3. Define a subset and confirm with OK. The subset displays in the project view. This subset is not saved with the project and does not modify the project. After closing the project view of the subset, the subset is lost.
However, you can save the subset as a separate project.
5.2.11 About Project Naming in Workspaces
Projects in workspaces have compound names that include the path to the image data.
Each folder within the workspace folder is part of the name that displays in the right pane of the Workspace window, with the name of the scene or tile included at the end.
You can easily observe the naming convention by opening each folder in the left hand pane of the Workspace window. The Scene name displays in the Summary pane of the Workspace window.
The name will also indicate any of the following:
• Whether the item is a tile.
• Whether the item is a subset.
• The scale, if the item has been rescaled.
• Whether the item is related to a well or a site.
To view the entire name, select List View from the drop-down list in the right pane of
View Data in Projects on page 94
Open a Separate Project on page 43
Subset Selection on page 464
Save a Project on page 55
Available only for
Definiens eCognition Life Server
the Workspace window.
Figure 62: Workspace window with folders open to display project naming.
5.2.12 Inspect the State of a Project
For control purposes you can view the state of the current version of a project.
1. Go to the right pane of the Workspace window that lists the projects.
2. Check the State of the current version of a project displayed beside its Name. The following states are possible:
Manage Projects in a Workspace on page 57
Processing States Related to User Workflow
Created Project has been created. Create a New Project on
page 44
Canceled Automated analysis has been canceled by the user. Cancel Image Analysis of Waiting and Currently Processing Projects on page 373
Edited Project has been modified or manually edited by the user. Modify a Project on page 54 Manual Editing on page 394 Processed Automated analysis has finished successfully. Process Data on page 363 Skipped Tile was not not selected randomly by the submit scenes for analysis
algorithm with parameter Percent of Tiles to Submit defined smaller than 100.
Reference Book
Stitched Stitching after processing has been successfully finished. Stitch Tile Results on page 380
Accepted Result has been marked by the user as accepted. Accept and Reject Results on page 394
Rejected Result has been marked by the user as rejected. See above.
Deleted Project was removed by the user. This state is visible in the Project History. Inspect the State of a Project on page 86
Other Processing States
Unavailable A basic element of the software, the Job Scheduler, where the job was submitted is currently unavailable. It might be disconnected or restarted.
Start Automated Image Analysis on page 365 waiting Project is waiting for automated analysis. See above.
processing Automated analysis is running. Cancel Image Analysis of
Waiting and Currently Processing Projects on page 373
FAILED Automated analysis has failed. See Remarks column for details.
TIMEOUT Automated analysis could not be completed due to a timeout.
CRASHED Automated analysis has crashed and could not be completed.
5.2.13 Inspect the History of a Project
Inspect detailed information for each version of a project. Inspecting older versions helps with testing and optimizing solutions. This is especially helpful when performing a complex analysis, where the user may need to locate and roll back to an earlier version.
1. To inspect the history of older project versions, go to the right pane of the Workspace window that lists projects. Right-click a project and choose History from the context menu. The Project History dialog box opens.
Figure 63: Project History dialog box.
2. All project versions (Ver.) are listed with related Time, User, Operations, State, and Remarks.
3. Click OK to close the dialog box.
Options
a Click a column header to change sorting by column.
b To open a project version in the Project View, do one of the following:
• Select a project version and click View.
• Double-click a project version.
5.2.13.1 Rollback a Single Project
S To restore an older version, choose the version you want to bring back and click the Rollback button of the Project History dialog box. The restored project version does not replace the current version but adds it to the project version list. The intermediate versions are not lost.
Inspect the State of a Project on page 86
5.2.14 Rollback All Changes of Projects
Rollback all changes to restore one or multiple projects to the first version.
Beside the Rollback button of the Project History dialog box, you can proceed as follows:
1. Do one of the following:
• Select a project in the right pane of the Workspace window and select Analysis > Rollback All on the main menu bar.
• Select a project in the right pane of the Workspace window and select Analysis > Rollback All on the main menu bar.