Help Index
The IIP3D viewer is used to display very large images on a web browser.
Images may be:
- Arbitrary sections through 3D images in the proprietry Woolz format.
- Stacks of pyramidal tiff images.
- A single pyramidal tiff image.
The visible part of the image, which may be only a small part of the complete image, consists of rectangular tiles supplied by an IIP3D server.
This is the default mode of the viewer, it may also be selected using the Context Menu.
Move mode supports the following user actions:
- Pan the image by clicking and dragging the left mouse button.
- Change the magnification by scrolling the mouse wheel.
Measurement mode is selected using the Context Menu. When it is selected the measurement dialogue box appears.
Measurement mode supports the following user actions:
- Measure between 2 user-selected points on the image.
Clicking the mouse over the image will cause a blue cross to be drawn (the measurement origin).
If the mouse is moved away from the measurement origin and then paused, the current distance will be indicated in the dialogue box.
Clicking the left mouse button over the image again will cause a second blue cross to be drawn. The distance between the crosses is indicated.
Note: the indicated value refers to the image at 1:1 magnification.
Equivalent Section mode is selected using the Context Menu. When it is selected the equivalent section dialogue box appears.
Equivalent Section mode supports the following user actions:
- Select the High Resolution section which passes through a user-selected point on a 3D image section.
Clicking the mouse over the image will cause a blue cross to be drawn on the image (the point through which an equivalent high resolution section passes).
The user must now click OK in the dialogue box to view the equivalent section.
Note: this action is only supported for 3D Woolz images where appropriate high resolution sections are available.
Fixed Point mode is selected using the Context Menu. When it is selected the fixed point dialogue box appears.
Fixed Point mode may also be selected from the rotation tool in the Toolbox.
Fixed Point mode supports the following user actions:
- Change the Fixed Point about which a 3D Woolz image rotates.
Clicking the mouse over the image will cause a blue cross to be drawn on the image (the new fixed point).
Closing the dialogue box will apply the new fixed point.
Note: the distance will be reset to 0 at the new fixed point.
Note: this action is only supported for 3D Woolz images.
The context menu is accessed by clicking the right mouse button over the image.
Clicking on the Help context menu item causes the following behaviour:
- This help page is displayed.
Clicking on the Reload Image context menu item causes the following behaviour:
- The IIP3D server sends the visible tiles of the image to the viewer again.
This is useful if, for example, the image is scrambled or incomplete.
There is also a Reload Image button in the Toolbox.
The Maximise Image context menu item is a toggle. Clicking on it causes the following behaviour:
- If the associated checkbox is un-checked the image borders will be extended to the edge of the browser window and the checkbox will be checked.
- If the associated checkbox is checked the image borders will be returned to their initial position and the checkbox will be un-checked.
The checkbox is initially un-checked.
If the image is large enough to fill the browser window, the Toolbox will be displayed on top of the image.
The Toolbox context menu item is a toggle. Clicking on it causes the following behaviour:
- If the associated checkbox is un-checked the Toolbox will be made visible and the checkbox will be checked.
- If the associated checkbox is checked the Toolbox will be hidden and the checkbox will be un-checked.
The checkbox is initially checked.
The Image Hover Feedback context menu item is a toggle. Clicking on it causes the following behaviour:
- If the associated checkbox is un-checked, feedback labels (provoked by hovering the mouse over an image) will be made visible and the checkbox will be checked.
- If the associated checkbox is checked, feedback labels (provoked by hovering the mouse over an image) will be hidden and the checkbox will be un-checked.
The checkbox is initially checked.
The Move Mode context menu item is a radio button. Clicking on it causes the following behaviour:
-
If the associated radio button is un-selected, the viewer will be set to Move Mode and the radio button will be selected.
All other radio buttons will be de-selected. - If the associated radio button is selected, clicking on it will have no effect.
The radio button is initially selected (this is the default mode).
The Measurement Mode context menu item is a radio button. Clicking on it causes the following behaviour:
-
If the associated radio button is un-selected, the viewer will be set to Measurement Mode and the radio button will be selected.
All other radio buttons will be de-selected. - If the associated radio button is selected, clicking on it will have no effect.
The radio button is initially un-selected.
When the radio button is selected the Measurement dialogue will appear.
The Equivalent Section Mode context menu item is a radio button. Clicking on it causes the following behaviour:
-
If the associated radio button is un-selected, the viewer will be set to Equivalent Section Mode and the radio button will be selected.
All other radio buttons will be de-selected. - If the associated radio button is selected, clicking on it will have no effect.
The radio button is initially un-selected.
When the radio button is selected the Equivalent Section dialogue will appear.
The Fixed Point Mode context menu item is a radio button. Clicking on it causes the following behaviour:
-
If the associated radio button is un-selected, the viewer will be set to Fixed Point Mode and the radio button will be selected.
All other radio buttons will be de-selected. - If the associated radio button is selected, clicking on it will have no effect.
The radio button is initially un-selected.
When the radio button is selected the Fixed Point dialogue will appear.
Fixed Point Mode can also be selected from the Toolbox Rotation control.
Mouse over the Query External Data context menu item causes the following sub-menus to appear:
-
By Anatomyup top
Mouse over the By Anatomy context menu item causes the following sub-menus to appear:
-
EMAGEup top
Clicking the EMAGE context menu item causes the following action:
- The Query Anatomy dialogue appears.
If Image Hover Feedback is enabled, hovering over the image will show anatomy components at the mouse position.
A left mouse click will initiate a query (on the indicated anatomy components) to the EMAGE Gene Expression database.
Query results returned from the EMAGE database will appear in a separate browser window. -
MGI-GXDup top
Clicking the MGI-GXD context menu item causes the following action:
- The Query Anatomy dialogue appears.
If Image Hover Feedback is enabled, hovering over the image will show anatomy components at the mouse position.
A left mouse click will initiate a query (on the indicated anatomy components) to the MGI-GXD database.
Query results returned from the MGI-GXD database will appear in a separate browser window.
-
-
By Spatial Regionup top
Clicking the By Spatial Region context menu item causes the following action:
- The Spatial Query dialogue appears.
Note: Spatial Query is not enabled in this version of the viewer.
Clicking on the Cancel context menu item causes the following behaviour:
- The context menu is hidden.
Clicking on the Reload Image button in the Toolbox causes the following behaviour:
- The IIP3D server sends the visible tiles of the image to the viewer again.
This is useful if, for example, the image is scrambled or incomplete.
There is also a Reload Image menu item in the Context Menu.
The Magnification control in the Toolbox is a slider.
Moving the slider cursor causes the following action:
- The magnification of the image is increased or decreased by a factor of 2.
The slider cursor may be moved by:
- Pressing the left mouse button over the red slider-cursor and dragging the mouse left or right.
- Clicking the left mouse button over the grey slider bar.
The Distance control in the Toolbox is a slider.
Moving the slider cursor causes the following action:
- The distance of the section plane from a fixed point in the image is increased or decreased.
The slider cursor may be moved by:
- Pressing the left mouse button over the red slider-cursor and dragging the mouse left or right.
- Clicking the left mouse button over the grey slider bar.
The Distance tool is supported for:
- 3D Woolz images.
The Key Sections control in the Toolbox combines the above Distance tool with Key Section arrow buttons.
Clicking on the various Arrow Buttons causes the following actions:
-
The first available section delineated with anatomy is displayed.
-
The previous available section delineated with anatomy is displayed.
-
The next available section delineated with anatomy is displayed.
-
The last available section delineated with anatomy is displayed.
The Key Section tool is supported for:
- 3D Woolz images comprising orthoganal sections, where some of the sections have been delineated with anatomy.
The Section Selector control in the Toolbox consists of a wholemount image with a red cursor bar through it. It also has arrow buttons.
Moving the red cursor bar, or clicking the arrows will cause the following action:
- A section from up or down the stack of images will be displayed.
Note that the section numbers may increase towards the top or towards the bottom of the image depending upon the way the stack has been constructed.
The Section Selector tool is supported for:
- Stacks of 2D pyramidal tiff images.
- 3D Woolz images comprising orthoganal sections.
The Locator control in the Toolbox consists of a thumbnail of the displayed image with a grey box indicating the visible region of the image.
The Locator control is used to alter the visible region of the image. This is done by the following user action:
- Press the left mouse button over grey box in the Locator control thumbnail, then drag the grey box to the desired location.
In some viewer modes it is also possible to press the left mouse button over the actual image and then drag the image to the desired location.
The Locator tool is supported for:
- 3D Woolz images.
The Rotation control in the Toolbox comprises 3 slider controls (pitch, yaw, roll) and 3 pre-set buttons (Trans, Sagit, Front).
Moving one of the slider cursors causes the following action:
- The appropriate viewing angle (pitch, yaw, roll) of the displayed section is increased or decreased.
Clicking one of the pre-set buttons on the Rotation control causes the following action:
- Trans The viewing angles (pitch, yaw, roll) of the displayed section are set for a Transverse section view.
- Sagit The viewing angles (pitch, yaw, roll) of the displayed section are set for a Sagittal section view.
- Front The viewing angles (pitch, yaw, roll) of the displayed section are set for a Frontal (or Coronal) section view.
Note that the actual values of pitch, yaw and roll will depend upon how the 3D image was re-constructed.
The Rotation control also has a button which opens the Fixed Point control.
The Fixed Point control displays the current X,Y,Z coordinates of the fixed point in terms of the underlying 3D Woolz coordinates.
The Fixed Point can be changed by the following user action:
- While the Fixed Point control is visible, click on the image at the required coordinates. A blue cross will appear and the new coordinates will be displayed in the Fixed Point control.
-
Click on the
close button at the top riight of the Fixed Point control to accept the new Fixed Point.
- Or click the Cancel button on the Fixed Point control to revert to the previous Fixed Point.
- Or click the Default button on the Fixed Point control to revert to the default Fixed Point (usually the centre of the image).
Note: The position in the displayed section determines the X and Y coordinates of the Fixed Point, the Z coordinate is determined by the current value of Distance.
Note: when the Fixed Point is changed, Distance is reset to 0.
The Rotation tool is supported for:
- 3D Woolz images.
The Layer tool in the Toolbox has a checkbox and a Properties button for each available layer.
The following behaviours are supported:
- If a layer's checkbox is checked, the layer will be displayed (although it may be obscured by another layer).
- The current selected layer is highlighted in blue in the Layer tool. This layer is not necessarily visible.
- If a layer represents a composite image, it must be selected and visible for any delineated regions to be visible.
- If the Layer button is clicked, the Properties tool will be displayed.
The Properties tool has a slider control for opacity and 3 slider controls for filtering red, green, and blue respectively.
Moving the slider cursor of the opacity control causes the following action:
-
The opacity (as determined by the browser) of the selected layer is increased or decreased.
If the image tiles delivered by the IIP3DServer are fully opaque then 0.0 on the opacity slider means fully transparent and 1.0 means full opaque.
If the image tiles delivered by the IIP3DServer have a pre-set opacity, then 1.0 on the opacity slider will give this pre-set value.
Moving the slider cursor of any of the 3 filter controls causes the following action:
-
The appropriate colour channel (red, green or blue) of the image is filtered to allow a maximum value between 0 and 255.
A filter slider value of 0 does not allow any of the colour through.
A filter slider value of 255 allows all of the colour through.
The Properties tool relates to the layer which is selected (highlighted in blue).
The Filter controls do not have any effect on composite images.
The Layer tool is supported for:
- Composite 3D Woolz images.
- 3D Woolz images with overlays.
- Multiple 3D Woolz images.
The Pitch Yaw tool in the Toolbox consists of a representation of the 3D Woolz image, intersected by a disc which represents the plane of the displayed image.
The angle of the disc through the 3D image provides visual feedback of the Pitch, Yaw and Roll angles set by the Rotation tool.
The Layer tool is supported for:
- 3D Woolz images.
The Tree tool contains an expandable tree which represents delineated regions in a 3D Woolz image.
The Tree tool supports the following behaviours:
-
Checking the checkbox of a node will cause the corresponding delineated region in the image to be highlighted according to the coloured box next to the node.
If the current section intersects the region, the intersecting area will be displayed, in the appropriate colour. - Un-checking the checkbox of a node will cause the corresponding region in the image to be hidden.
-
Clicking on the coloured box next to a node will open a colour chooser which enables the colour associated with a delineated region to be changed.
If the colour of a node is changed, this will be reflected immediately in any part of the appropriate delineated region which is visible.
There are 2 buttons at the top of the Tree tool which have the following behaviour:
-
The Select All button causes the checkbox of every node with a corresponding delineated region to be checked.
If the current section intersects any of these regions, the intersecting areas will be displayed, in the appropriate colour. -
The Clear All button causes the checkbox of every node with a corresponding delineated region to be un-checked.
No delineated regions will be visible.
Double-clicking over a part of the image which has a delineated region will cause the checkbox of the corresponding node to be checked / un-checked.
The Layer tool is supported for:
- composite 3D Woolz images.
- 3D Woolz images with overlay.
The Scalebar tool consists of a horizontal line (black on top of white) with the length of the line indicated above it.
The scalebar can be dragged around the image by pressing the left mouse button over the scalebar, then dragging the Scalebar to the desired location.
The indicated length of the line is with respect to the undelying image at scale 1:1.
The Scalebar tool is supported for:
- 3D Woolz images.
- Stacks of 2D Pyramidal Tiff images.