Start Multiple Clients
2.1. First select the correct driver in the Files of type drop-down list box
Figure 30: Select a Driver.
2.2. Then select from the main file in the files area.
If you select a repository file (archive file), another Import Image Layers dialog box opens in which you can select from the contained files.
Figure 31: Import Image Layers dialog box listing items of a repository file.
Press Open to display the Create Project dialog box.
RGB on page 490
Create New Project Create a New Project Within a Workspace on page 89
Supported Image Formats on page 47
Import Image Layers on page 452
Figure 32: Create Project dialog box.
3. The project header area ` displays project properties concerning pixel size, coordinate system, geocoding and other.
4. All preloaded image layers are displayed a along with their properties.
5. Click OK b to create the new project. If a workspace is open, the new project is displayed in the right pane of the Workspace window. Otherwise, the image is displayed in the project view.
Options
c Edit the Project Name.
d Define or clear a subset if the complete image to be analyzed is relatively large and you want to work on a smaller area to save processing time. For details, see section Subset Selection.
e If you want to rescale the scene during import, edit the scale factor in the text box corresponding to the scaling method used: Resolution (m/pxl), Magnification (x), Percent (%), or Pixel (pxl/pxl).
f To use the geocoding information from an image file to be imported, select the Use geocoding checkbox.
g For feature calculations, value display, and export, you can edit the Pixels size and select another Unit. If you keep the default Auto, the unit conversion is applied according to the unit of the coordinate system of the image data as follows:
• In case of included geocoding information, the pixel size is equal to the resolution.
• In other cases, pixel size is 1.
In special cases you may want to ignore the unit information from the included geocoding information. To do so, deactivate the Initialize unit conversion from
Subset Selection on page 464
About Scales on page 49
Options on page 456
input file item of the Options dialog box.
a List of image layers. To select an image layer, click it. To select multiple image layers, press Ctrl and click on the image layers.
h To insert an additional image layer, do one of the following:
• Click the Insert h button.
• Choose Image Layers > Insert on the menu bar of the dialog box.
• Right-click inside the image layer list a and choose Insert on the context menu.
The Import Image Layer dialog box opens. Select the desired data.
To remove one or more image layers, select the desired layers and click Remove.
i Select an image layer and use the up and down arrows to change the order of the layers.
a You can edit layer aliases. Double-click or right-click an image layer and choose Edit. The Layer Properties dialog will open.
j Alternatively you can click the Edit j button.
k To set the value of those pixels that are not to be analyzed, click No Data. The Assign No Data Values dialog box opens.
l If you import image layers of different sizes, the largest image layer dimensions determine the size of the scene. When importing without using geocoding f, the smaller image layers are handled as follows: Smaller image layers keep their size if the Enforce Fitting check box is cleared. If you want to stretch the smaller image layers to the scene size, select the Enforce Fitting check box.
m Load Metadata files. Click the Select button to edit the path. An Import Metadata dialog box opens, where you can select a file.
When importing metadata you must convert available external metadata to an internal metadata definition. Select an item in the list and click the Edit button to open the Metadata Conversion dialog box.
To remove a metadata file, select and click the Remove button.
Thematic Layer Options
n To insert a thematic layer, do one of the following:
• Click the Insert n button.
• Choose Thematic Layers > Insert on the menu bar of the dialog box.
• Right-click inside the thematic layer list o and choose Insert from the context menu.
The Import Thematic Layer dialog box, which is the equivalent of the Import Image Layers dialog box, opens.
o List of thematic layers. To select a thematic layer, click it. To select multiple image layers, press Ctrl.
o You can edit thematic layer aliases. Double-click or right-click a thematic layer and choose Edit. The Layer Properties dialog will open.
p Alternatively you can click the Edit p button.
n To remove one or more image layers, select the desired layers and click Remove.
About Layer Aliases on page 54 Provide it to the Feature Tree on page 52
Work with Thematic Layers on page 284
Layer Properties on page 452
q If you use more than one thematic layer, select a layer and use the up and down arrows to change their order.
Note
There is no option to assign No Data Values for thematic layers.
5.1.2.1 Supported Image Formats
Various file drivers enable you to import the following image data formats:
Import File Format (Driver) File
Microsoft Windows Device Independent Bitmap
.bmp - 4 GB No Yes Yes RW X X
Military Elevation Data .dt0 .dt1
[1] Georeferencing is supported, though there may be some limitations in support of datums and ellipsoids. If ground control point (GCP) segments are present, the first will be used, and the rest ignored.
[2] In order to import images from an Aperio slide scanner in Definiens clients, Aperio ImageScope product must be installed on the client machine. Furthermore, in order to do batch processing of Aperio slide scanner image data, Aperio ImageScope must be installed on each physical server running as a processing node. If you do not already have ImageScope, you can download it from the Aperio website.
Other formats are available on request. Contact the Definiens sales team at [email protected].
Note
For best results, we recommend use of uncompressed image formats because the information content is of higher quality than in formats using a compression that loses data. For example, an uncompressed .tif file will produce better analysis results than a compressed .jpg file.
Note
All import formats supported for image layers also apply for thematic layers.
Additionally, .shp vector files are supported.
http://www.aperio.com /download.asp
For polygon shapefiles and for .img files, the attribute table is automatically selected.
For all other formats the respective attribute table has to be specifically indicated.
From the Load attribute table dialog, the following file formats can be selected:
• .txt ASCII text files
• .dbf Dbase files
• .csv Comma separated values files
5.1.2.2 Maximum Image Size
The image size is limited theoretically, to 262 pixels. However, testing has been performed only on images up to 20 gigapixel (141 421 x 141 421 = 234 pixels) only.
Furthermore, you have to consider limitations in processing large projects while executing an image analysis.
5.1.2.3 About Scales
The scale of a scene or of image data describes the ratio of the depicted distance to the distance in reality. When working with scenes in projects and workspaces, Definiens Developer provides different types of scale modes used for displaying and calculating scale factors.
Scale Mode Description Example
Unit (m/pxl) Resolution expressed in meters per pixel. 20 m/pxl Magnification Magnification factor used similar as in microscopy. 20x Percent Relation of the scale to the original scene scale. 20%
Pixels Relation of pixels to the original scene pixels. 1:20 pxl/pxl You can set the type of scale mode in the Options dialog box under the Display scale with item.
You can check the scale mode in the following displays:
• Scale column in the right pane of the Workspace window
• Scale text box in the Create Project and Modify Project dialog boxes located below the Subset buttons
• For Magnification only, the Zoom combo box changes.
The scale mode is used for calculating scaling operations when creating scene copies or copies of scene subsets.
About Processing Limitations on page 373 How to Handle Large Data Sets on page 348
Options on page 456
Manage Projects in a Workspace on page 57
Create a New Project on page 44
Modify a Project on page 54
Zoom
Zoom to a Magnification Zoom Value on page 105
Work at Different Scales on page 376
Rescaled Scene Copy on page 303
Rescaled Copy of a Scene Subset on page 304
Note
The scaling results may differ depending on the scale mode. Example: If you enter 40, you work at the following scales, which are calculated differently:
Options dialog box setting Scale of the scene copy or subset to be created Units (m/pixel) 40m per pixel
Magnification 40x
Percent 40% of the resolution of the source scene Pixels 1 pxl per 40 pxl of the source scene
5.1.2.4 Import Image Layers of Different Scale
You can insert image layers and thematic layers with different resolutions (scale) into Definiens Developer.
They need not have the same number of columns and rows. To combine image layers of different resolution (scale), the images with the lower resolution—having a larger pixel size—are resampled to the size of the smallest pixel size. If the layers have exactly the same extent and geographical position, then geocoding is not necessary for the resampling of images.
Figure 33: Left: Higher resolution - small pixel size. Right: Lower resolution - image is resampled to be imported.
5.1.2.5 About Geocoding
Geocoding is the assignment of positioning marks in images by coordinates. The position marks serve as geographic identifiers. but geocoding is helpful for life sciences image analysis too. Typical examples include working with subsets, at multiple
magnifications, or with thematic layers for transferring image analysis results.
Geocoding information is automatically detected by Definiens Developer or can be entered manually. Images without geocodes create automatically a virtual coordinate system with 0/0 upper left and the unit of 1 pixel. For such images, geocoding represents the pixel coordinates instead of geographic coordinates.
Definiens Developer cannot reproject image or thematic layers. Therefore all image layers must belong to the same coordinate system in order to be read properly. If the coordinate system is supported, geographic coordinates from inserted files are detected automatically. If the information is not included in the image file but is nevertheless available, you can open a dialog for each layer to insert the geocoding information
Layer Properties on page 452
manually by double-clicking the appropriate layer or right-clicking and choosing Edit.
This opens the Layer Properties dialog box.
Figure 34: The Layer Properties dialog box allows you to edit the geocoding information.
5.1.2.6 Multisource Data Fusion
If the loaded image files are georeferenced to one single coordinate system, image and thematic layers with a different geographical coverage, size or resolution can be inserted.
This means that image and thematic data of various origins can be utilized
simultaneously. The different information channels can be brought into a reasonable relationship to each other.
Figure 35: Layers with different geographical coverage.
5.1.2.7 Convert Metadata to Provide it to the Feature Tree
When importing data, you can provide a selection of available metadata. To do so, you have to convert external metadata to an internal metadata definition. This provides a selection of the available metadata to the feature tree and enables its usage in rule set development.
When developing rule sets, metadata definitions will be included in rule sets, enabling the serialization of metadata usage.
1. When importing metadata you must convert available external metadata to an internal metadata definition:
• Within the Create Project dialog box, go to the Metadata group. After loading and selecting a metadata file, click the Edit button to open the Metadata Conversion dialog box.
• Within the Customized Import dialog box, go to the Metadata tab and select Conversion settings. Click the ellipsis button to open the Metadata
Conversion dialog box.
2. Click the Scan Metadata button to display available external metadata items in the left column and the related internal metadata item name in the right column.
Figure 36: Metadata Conversion dialog box displaying sample metadata items.
3. The Image Layer Aliases group lists metadata items concerning image layers aliases.
4. The Values group below lists metadata items which can be selected for display in the feature tree. Select a metadata item and click the drop-down arrow button placed inside the right field. Select an existing feature from a drop-down list to be used as the name of the internal metadata item.
5. Alternatively, you can select <create new feature> from a drop-down list. The Parameter Configuration dialog box opens.
Create a New Project on page 44
Metadata Import Options on page 72 (ellipsis button)
Figure 37: Metadata Item dialog box.
6. Define Name and Type of the internal metadata item. Click OK to create the feature.
7. To create features for all listed metadata items, click the Generate All button. All features are created as string item with the same name as the metadata item. To modify a feature, select one meta data item and click the drop-down arrow button.
Select <create new feature> from the drop-down list to open the Parameter Configuration dialog box for editing.
8. After reconfirming and closing the internal metadata is displayed in the feature tree, for example in the Feature View window. Here you may also edit the features, if you need to.
Options
9. List the values of metadata items by clicking the Values button. To go back to the list of internal names, click the Names button.
10. You can convert selected values of a metadata item. This enables you to use an internal value which is different from the external values.
To do so, select a metadata item and click the Insert Value Conversion button. The Enter External Value dialog box opens asking for the external value that you want to be converted. It will be added in a Value Conversion sub group below the metadata item. In the Internal column on the right, you can edit the internal value to be used instead of the external value.
Figure 38: Value conversion of the metadata item PROJECT_NAME in the Metadata Conversion dialog box.
11. If you want to save the conversion settings of the Metadata Conversion dialog box