1. Setup

Overview

In the Setup step, enter information about the slide you want to image and the type of scan that you want to perform. You also specify where and how to store the data and image files that you will acquire using the workflow.

Before you start

Put your slide on the microscope and place a reference point.
If you already have a data file associated with the specimen, be sure to place your reference point at the same location, otherwise you may need to realign the data with the live image.

Procedure

Each section of the workflow requires that you choose options or indicate file names and locations. Review the workflow window and record your desired slide scan setup.

Acquire type

Select the type of image acquisition:

2D slide scan: Acquires one image plane at each acquisition site
3D slide scan: Multiple image planes at each acquisition site are acquired to create image stacks. This choice is generally suitable for higher magnifications, but can also be used at lower magnification. (3D is only available if you purchased the 3D slide scanning module.)

Illumination type

Choose the illumination type for the slide (brightfield or fluorescence). This will affect the options available for background correction.

Multichannel acquisition

Multichannel: Check the box to acquire more than one color-channel.

This option is not available if there are no available settings for multiple color-channels; click the Multichannel setup button to define settings and enable multichannel image acquisitions.

Multichannel setup button: Click the button to open the Multichannel Setup window where you can define image-acquisition settings for the multiple color-channel slide scan.

This option is disabled when you select Brightfield as the slide type.

To acquire a single color-channel image set, the Multichannel box should NOT be checked.

Scan type

Scan inside contour only: Captures image tiles in the contour(s) that are drawn in step 4. Choosing this option may generate images with jagged borders but it minimizes processing time and file size.
Scan a rectangle around the contour: Generates rectangular images by capturing image tiles in a rectangle that contains the entirety of contour(s) drawn in step 4. Acquisition time and file size are increased relative to scanning inside the contour only.
Scan in a grid that is: Type in the number of fields of view (X, then Y) to include in the scan.
- You must be positioned at the top left corner of the region to be scanned; the current field of view is the first one scanned.
- When this option is selected, the workflow skips step 6. Region selection.

File locations

Data file location: Click Browse. The Save As window opens; indicate the desired file name, location, and type for the data associated with the scan, then click Save.

We recommend choosing XML Document File (*.xml) as the file type.
Image file location: Click Browse.The Save As window opens; indicate the desired file name, location, and type for the images or image stacks associated with the scan, then click Save.
- We recommend choosing MBF JPEG2000 (*.jpx or *.jp2) as the file type.
- Note that if you choose Tiff (*.tif) as file type, image scaling will not be embedded.
Enable background tile copy to remote location: Check the box to save copies of the individual image tiles from your slide scan to a remote computer drive, i.e., not the computer that runs the microscope/Neurolucida.
- Click Browse. The Choose a Folder window opens; navigate to the desired drive and select a folder or make a new folder to store the files, then click Select Folder.
- Delete source tiles after copying to remote location: Check the box to delete the individual image tiles from the microscope-connected computer after they have been saved to the remote location.