Table of Contents
BioImage is divided into three main panes: the Processing Pane on the left, the Visualization Pane in the center, and the Visualization Settings Pane on the right as shown in Figure 1.1. The two side panes can be detached from the Visualization Pane by clicking on the pane detachment/attachment controls. These are the vertical dashed lines separating the panes. Detaching these panes allows the user to resize the Visualization Pane for better viewing.
The Processing Pane guides the user through processing their data for visualization. It has two top-level menus: File and Help. The File menu items Save Session... and Load Session... allow the user to stop and resume BioImage sessions. After loading a saved session with Load Session..., resume processing and visualization by clicking Update. The Restore Panes File option (or Control-R) will bring any detached Panes that have been hidden or closed to the front of the screen. The Help menu item Show Tooltips toggles tooltips. "Hovering" the mouse pointer over a control displays a tooltip describing a control.
Under the Processing Pane menus are the filter buttons. These buttons allow the user to add steps to a dynamic pipeline. See “Dynamic Filters” below for more information regarding adding filters to the pipeline.
Directly below the filter buttons, is a scrolled window containing the History of steps in the user's dynamic pipeline. A BioImage pipeline will always contain a Load section as the first step in the pipeline. See Chapter 5, Data Input for more information regarding loading data. Any filters added by the user will appear in the pipeline with their unique UI.
Not every user's pre-processing steps will be the same nor in the same order. One user may want to crop first then resample while another may prefer to resample first and crop later. BioImage does not impose an order to the processing steps. The user can add and delete steps to form the desired pipeline. This pipeline is represented in the History section of the Processing Pane.
The history will always start with a Load Data step and corresponding user interface. All subsequent filters will appear under the Load Data UI.
Each filter UI contains four main components as shown in in Figure 4.1: the visibility icon to collapse or expand the filter UI, the filter label, insert bar, and close button. In addition to these four things, each filter contains a unique interface representing its particular parameters.
The visibility icon is located in the top left of each filter UI and is labeled 1 in Figure 4.1. This icon controls whether the entire filter UI is displayed and in full view or just the label and close button. By clicking this icon, the user can hide or show the filter UI.
To the right of the visibility icon is a label which will remain visible whether the UI is in full view or hidden. It is labeled 2 in Figure 4.1. The label defaults to be the string "Filter - Unknown". By right clicking on the label, the user can edit the label to be something more meaningful. This is especially useful when a pipeline contains many instances of the same type of filter.
The red close button, labeled 3 in Figure 4.1 will delete the filter from the pipeline. See the section Deleting Filters for more information.
The insert bar is used for inserting new filters between existing filters and is discussed more in the Adding and Inserting Filters section. It is shown by the label 4 in Figure 4.1
There are two ways to add a new filter to the pipeline. The first approach is to click the button for the corresponding filter. These buttons are located directly above the history section as shown in Figure 4.2. When clicking one of these buttons, the filter will always be added to the end of the pipeline.
The second approach to adding filters to the pipeline allows the user to insert a filter between two existing filters. One of these filters may also be the Load Data step. To insert a filter, the user must click the blue bar which separates the two filters, causing a menu of available filters to appear. Selecting one of these filters will add the appropriate filter in the specified location into the pipeline.
The red close button is located in the top right corner. Clicking this button will delete the filter from the pipeline and remove the UI from the history. All settings for that filter will be lost. Since there must always be data to process, the Load Data UI does not have the close button.
The radiobuttons to the left of the insert bars indicate the currenlty viewed data or the eye. Changing the eye allows the user to view input and output data to a filter. For example, if the radiobutton below a crop filter is selected, the cropped image will be shown in the Visualization Pane. If the radiobutton above a crop filter is selected, the un-cropped dataset will be shown. As filters are added or inserted, the eye will update to be the set to the output of the new filter. It is especially helpful when editing Crop value to have the eye selected for the Crop filter being edited.
Anytime a filter parameter has changed, the user must click the green Update button located towards the bottom of the Processing Pane to see the results. The Update button is only enabled when a change has been made which requires re-execution.
The bottom of the Processing Pane contains a Progress Indicator, a text description indicating the current state of the application, and suggests the next processing step. The Progress Indicator indicates an error if an error occurs. Clicking on the Progress Indicator displays an error log.