Turboscan / Turboscan Compiler
Overview
Neurolucida is combined with Objective Imaging technology (OASIS and Turboscan) to synchronize image acquisition with stage movement for scanning large brightfield images significantly faster.
What you need
- OASIS blue card for the stage controller
- License for Turboscan
- Camera with trigger cable
The Turboscan workspace
Although you are working in Neurolucida, you'll be using tools designed by Objective Imaging: 
- Map window (used to define and implement scanning).
- Select to define a rectangular region of interest (ROI).
- Drag the mouse to draw a rectangle.
- Select to define the scan pattern (grid) area to be used for the scan.
- Drag the mouse to draw the grid.
- Turboscan panel (enables the interactions between Neurolucida and OASIS)
- JoyTools panels (used to select lenses, instead of the drop-down menu in Neurolucida)
- Live Video window (instead of Live Image in Neurolucida)
Map window toolbar
The tools you're most likely to use are highlighted in yellow in the table below. 
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Moves the scan pattern (grid) to the current stage location. |
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Fit the entire stage in the view. |
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Deletes the scan pattern (grid). |
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Fit the background Prescan pattern as well as the Prescan image (if any) in the view (inactive). |
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Clears the scanned tiles (mosaic) to perform a new scan. |
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Fit the foreground scan pattern (grid) and scanned tiles (if any) in the view. |
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Clears the Prescan images from the background (inactive). |
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Sets the Map window zoom level to be the equivalent of the chosen objective magnification. |
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Predictive Focus: Use the dialog to define a series of focal points around the tissue; their correct focus positions in Z are stored. The positions of the other points are interpolated during scanning. |
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Hows/hides the lines of the scan pattern. |
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Performs a scan. |
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Default selection tool. Select it to disable clickable events in the Map window. |
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Moves the stage through each field of the scan pattern (grid) in sequence.Useful to inspect each field prior to scanning. |
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Stops a scan in progress. |
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Moves the stage to the first field of the scan pattern (grid). |
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Moves the stage to the mouse-clicked position in the Map window. |
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Moves the stage to the last field of the scan pattern (grid). |
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Moves the stage to the center of the field that you click in the Map window. |
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Currently disabled (Objective Imaging) |
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Adds an individual field to scan at the location clicked in the Map window. |
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Left-click to zoom in the view, right-click to zoom out. | ||
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Pan. | ||
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Drag the current scan pattern (grid) to re-position it. | ||
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Expands the scan pattern (grid) to encompass the current stage position. No effect if the current position is already within the scan pattern. |
Procedure
Step 1: Scan at low power to create a preview of the entire specimen.
- Select Acquisition>Turboscan.
- You are prompted to initialize the stage. Click OK.
- Neurolucida evaluates the stage limits.
- The Live Video window and several panels are displayed: Turboscan, Map, and JoyTools.
- You are prompted to initialize the stage. Click OK.
- Select a low power objective (e.g., 4x) at the microscope and, in JoyTools, select the corresponding lens from the drop-down menu .
- In Turboscan, select Image>Image setup to display the camera settings.
- Adjust the exposure and the balance, then click Apply
- Adjust the exposure and the balance, then click Apply
- Define the area to scan.
- Use the joystick to drive the stage to the top right corner of the slide.
- In the Map window, Click the Draw Scan Pattern icon.
- Drag the mouse to draw a Scan Pattern rectangle around the area to acquire.
- Drive the stage to the top left corner. The stage location is indicated by a small target icon in the Map panel.
- If the target icon is not inside the rectangle, click the Include XY position in Pattern icon to expand the rectangle and include the corner.
- If the target icon is not inside the rectangle, click the Include XY position in Pattern icon to expand the rectangle and include the corner.
- Drive the stage to the bottom left corner.
- If the target icon is not inside the rectangle, click the Include XY position in Pattern icon to expand the rectangle and include the corner.
- In the Map window, click the Run Scan button to start the acquisition.
- Select the Turboscan Stepped mode from the list.
In this mode, the stage stops at each field of view. - As tiles are scanned, a preview appears in the Scan Pattern rectangle in the Map panel.
- Select the Turboscan Stepped mode from the list.
Step 2: Scan an area of interest at a higher power.
- In the Map window, define the area to scan.
- Click the Draw Scan Pattern icon.
- Drag the mouse to draw a Scan Pattern rectangle around the area to acquire.
- To modify the scan pattern, right-click over the grid.
- Click the Clear mosaic icon to clear the scanned tiles.
- Click the Draw Scan Pattern icon.
- Click the Move to Stage XY icon to enable stage movement: When you click a point in the Map window representing the stage, the system automatically drives the stage to the desired location.
- Select a higher power objective on the microscope (e.g., 10x) and, in JoyTools, select the corresponding lens from the drop-down menu .
- Adjust the camera settings and apply background correction.
- Use the Live Video window and the joystick to find a blank area in the area of interest.
- In the Turboscan panel, select Image>Image Setup to display the camera settings.
- Use the Exposure and Balance tabs to make adjustments.
- Use the Shading tab to apply shading (i.e., background correction) for brightfield.
- Implement predictive focusing.
- In the Map window, click the Show Predictive Focus Dialog icon.
You are prompted to initialize focus. 
- Click OK. You are prompted to focus manually and to enter the upper and lower limits for the focus range.
- Click the Show Predictive Focus Dialog icon again to display the Predictive Focus Setup panel.
- Check the Enable Predictive Focus box.
- Use the joystick to select a focus point on the slide.
- Click Add. The focus point is indicated by a red target on the scan grid.
- Focus manually and click Update. The red target turns green.
- Use the joystick to select another focus point on the slide.
- Repeat steps iii-v for as many focus points as needed.
- Click OK.
- In the Map window, click the Show Predictive Focus Dialog icon.
- In the Map window, click the Run Scan button to start the acquisition.
- Select the Turboscan Stepped mode from the list. The acquisition starts.
- Once the acquisition is done, use the Zoom and Pan icons in the Map window to verify that the quality of the acquired image is satisfactory.
- Once you've clicked the Zoom icon, left-click to zoom in and right-click to zoom out.
- In the Turboscan panel, select File>Save workspace to save the series of scanned tiles in a .sws file.
- Select File>Exit.
Step 3: Assemble the tiles into an MBF JPEG2000 image
- In the Neurolucida menu, select Acquisition>Turboscan Compiler to assemble the tiles into a single image.
- Select the .sws file you saved after scanning and click OK.
- The new image doesn't open automatically. To view the assembled image, select File>Image Open in the Neurolucida menu.