When you start Gumbo, you should see a window that looks like this:

1. First, you must connect to an iScope server by clicking the "connect" button. This version of Gumbo can connect only to our system at iscope.nervenet.org.
2. Once connected, please read through the information about the iScope system and the microscope descriptions. The last few lines of the microscope description box describe the current status of the microscope. If the microscope is currently reserved for another user, you can check and see if the other microscopes are available or schedule yourself for the next available time slot.
3. In order to reserve time on a microscope, you must login by entering your username and password in the appropriate boxes and then click the "Reserve Next Available" button. If you do not have a username and password, please select one here.
4. If the scope is available, you can now control the microscope by clicking on the "Control Scope" button. If it is currently in use, wait until the start of your time slot, login, and then click "Control Scope." Since the iScope is currently in a testing and debugging stage, all sessions are limited to ten minutes.

You should now see Gumbo's main navigation window:

1. The two low resolution images on the left allow you to quickly navigate to any location on the slide. The red box shows the location of the current video image, as well as the physical location of the microscope stage. The green circle can be dragged to a new location on either image; it serves as the target destination of any move operation.
2. These boxes reflect the current x and y coordinates of the green circle. If you do not want to use the images to navigate to a new location on the slide, you can type new values in these boxes and the images will update accordingly.
3. Clicking the "Show Current Position" button will return your target to the microscope's current location.
4. In order to actually move the microscope, you must click the "Move" button. This will cause the microscope to move to the location of the green box in the navigation images and to the Z-axis coordinate entered in the "Z" box. The new image will appear in the Video window.
5. Gumbo provides several different methods to focus the microscope. The "Quick Focus" button performs a quick scan of the tissue and moves the scope to the first likely in-focus plane. This focus algorithm can be fooled by dirt or bubbles that appear before actual tissue does. The "Accurate Slow Focus" uses a more reliable, but slower, focus algorithm which samples the entire focal range before returning. If the "Quick Focus" homes in on dirt or bubbles, you may want to use the "Accurate Slow Focus" to find the actual tissue.
6. Gumbo also provides a method for manually focusing the microscope with the "Get Focus Stack" button. This function creates a small preview movie based on the parameters entered by the user. After the movie is created, you can scan through it by moving the scrollbar. The Z-axis target box will update along with this movie, so when the desired focus is reached in the movie, you can click "Move" to retrieve a new full image.

Now that you can obtain a focused image from the microscope, it is time to look at the options provided in the Video window. Please note that in the current version of Gumbo (2.01) movie queueing and image export are disabled.

1. Gumbo provides several options for enhancing certain aspects of the image. Select an option to apply it to the image. The gain slider will not affect the image unless it is enabled with the Gain checkbox. Note: Contrast expansion may not work properly in the Windows release.
2. The red box, which can be toggled by clicking the "Focus Overlay" radio button, selects the region used for the focus stack discussed above.

I still don't understand what something does.

Please contact us: We would like to hear about any problems or suggestions you may have for Gumbo or the iScope. Please email either Michael Connolly or Tony Capra.