The StackViewer

The StackViewer is the full-screen tool for looking at stacks.

It has a number of operational components, numbered in the above diagram.

1. Breadcrumbs

The Sundog logo hides the breadcrumb trail; hover over to reveal it. If the breadcrumbs are cropped by the white box, you can scroll the box (vertically or horizontally, it doesn’t matter) to reveal them.

2. Manage Stack button

Clicking this button will reveal the “manage stack” menu. The manage stack dialog has a number of tabs

• manage layers allows you to delete layers from the stack, and specify which layer should be used to derive the scale. (The scale itself is derived from the metadata set in the file)
• add layers allows you to add more layers to the stack after you’ve made it. Only upload pages of the same dimensions, within the same experiment, will be shown.
• stack settings allows you to edit the Stack’s name, or delete the Stack entirely
• ** color labels** allow you to give each of the ten colors in the stackviewer names. These names will only apply to this particular stack. The names will appear in the color picker (see below).
• export data allows you to export annotations geometry or comments data as CSV/JSON. This will include co-ordinates in the original co-ordinate space of the image, as well as ids of which user made the comment/annotation, and (in the case of annotation) what colour they are (including the color’s name, if set).

3. Scale

The scale updates dynamically as you zoom the image. By default, the scale is derived from the top layer, but this can be changed in the manage stack dialog.

4. Main menu

Exactly as on the rest of Sundog, your own avatar is the main menu.

The avatars of any other users currently looking at this Stack will appear next to yours. Hover over them to see their name.

5. Navigator

The navigator shows the totality of the image you’re looking at, regardless of the zoom level. Click or drag it to quickly navigate the image. It hides while your mouse cursor is still.

6. Toolbar

The toolbar contains controls for working with the stack. All the tools apart from clipboard are sticky - after clicking on a tool you will stay in that mode until you select another non-clipboard tool, or press esc.

From left to right, the toolbar is:

• arrows - Navigate the image. Drag to navigate the image; use mousewheel or two-finger scroll to zoom in/out of the image. While in arrow mode, you can click to select an annotation, or click a comment thread to open it. Note that you only manipulate (edit/delete) annotations you have made yourself. Shift click an annotation to reveal the edit handles
• comments - make a comment. Click anywhere to start a new comment thread; once you’ve added a first comment in the thread, other people will be able to expand it to reply. You can leave comments on top of annotations.
• point - leave a point marker/pin. Points appear in your Personal Color.
• rectangle - draw a rectangular annotation.
• polygon - draw a polygonal annotation.
• clipboard - Copy the current view in the StackViewer to your clipboard. This only copies layer data - it will not copy annotations. Hold option/alt to save the current view as a file on disk when you click - the icon will change to a disk to indicate this.
• delete - delete an annotation by clicking on it. (There is currently no undo.)
• color picker - pick what colour your annotation will be. You can choose from a list of ten pre-set colours. This colours can be given names via the Stack Manager, which enables them to be used for categorisation/classification. If an annotation - point, rectangle, or polygon - is selected, the color picker will update to reflect its color. If the color picker is changed when an annotation is selected, it will update the color picker of the selected annotation.

Here, we can see the color picker expanded. Two of the colors have been given labels in the Stack Manager - these will be included in any data export.

7. Layers

All layers are shown in the palette. By default, the panel is closed; click the caret/arrow (a) to toggle the Layers panel. Scroll the panel with two-finger-scroll/scrollwheel to reveal more layers.

On each layer:

• grab the drag handle (b) to reorder the layers. Note that you cannot re-order annotations; they always appear on top.
• click the eye (c) to toggle layer visibility. You can toggle the visibility of annotations, but this is not shared with other users.
• click the layer name (d) to edit the name of the layer. (This is initially derived from the upload naame)
• click the fader icon (e) to bring up the layer control panel (f)

Layer controls

The layer control panel (f) lets you perform basic, non-destructive alteration to a Stack Layer:

• Opacity - transparency of this layer, where 0 is completely transparent and 1.0 (default) is opaque
• Contrast - adjust the difference between light/dark of a layer.
• Gamma - adjust the gamma curve of a layer: this alters contrast only in midtones. Contrast is more pronounced as gamma gets closer to zero (smaller).
• Brightness - boost/attenuate the level of every pixel. You probably don’t want this.
• False color - enable to false-color a layer. Click the color box that appears to pick a color. Only recommended with monochrome layers: it essentially turns a layer that is (black-to-white) to (black-to-color)
• Additive blend - turning this on will make black areas in the layer transparent (more accurately: all pixels will becoming transparent based on their relative brightness). Useful for turning a layer into an overlay, and particularly when combined with false-color.

Double click any slider to return it to its defaults.

Keyboard shortcuts

There are a number of keyboard shortcuts in the layer viewer, most notably for zooming the image and for picking tools. Press Question Mark ? Question Mark ? ( shift + Slash shift/ shift + Slash shift/ ) on the StackViewer page to view them.

They can also be seen in the Stackviewer Keyboard Shortcuts reference.

Comments, notifications, and mentions

When you leave a comment on a thread, anyone who is subscribed to a thread and has email alerts enabled will be notified. The creators of the thread and its parent stack are automatically subscribed to it, as is anyone who replies to the thread.

If you no longer want to receive notifications on a particular thread, you can click on the ... icon at the top of thread, which will display a menu that allows you to toggle subscription status (and to copy and paste the current URL).

Once you have unsubscribed using this option posting further comments on the thread won’t automatically re-subscribe you, but you can still explicitly re-subscribe using the menu item.

To draw someone’s attention to a comment when they aren’t already subscribed, you can mention them by typing ”@” followed by the first few letters of their name. This will suggest a list of users to mention. Picking one will add the mention to the comment and when the comment is inserted the mentioned user will be notified via email, providing they have email alerts turned on.

Note that mentioned users are not automatically subscribed to the thread. If they want to receive notifications after the initial mention, they can either explicitly subscribe via the menu toggle or just respond to the mention by leaving a comment.