Learn how to use the iScope software to control our microscopes and acquire images
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||Gumbo v2.8 Tutorial
When you start Gumbo, you should see a window that looks like this:
- First, you must connect to an iScope server by entering your username and password
in the appropriate boxes and clicking the "Connect" button. If you do
not have a username and password, please select one here.
This version of Gumbo can connect only to our system at iscope.nervenet.org.
Note that the button has been changed from "Connect" to "Refresh" after successful connection.
- 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.
- You can now reserve time on a microscope by clicking the "Reserve Now" button if the selected microscope is available.
But, all sessions are limited to 10 minutes if you reserve time by means of "Reserve Now".
- 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."
- The scope session will exit by clicking "Exit" button.
- If you want to reserve more time or other preferred time on a microscope, you should click "Scheduling..." button.
A message dialog will inform you the maximum controlling time for your selected microscope. The maximum controlling time is controlled by
the iScope server. It could be adjusted based on the status of each microscope. After clicking "Ok" on the message dialog, you
should see the following window.
Now, let's look at Gumbo's main navigation window, which should show up after clicking on the "Control
- You can select the desired start date and time and the duration of scope use between 1 minute and the maximum controlling time in the appropriate boxes.
- In oder to sucessfully reserve time, you are recommended to click "Refresh Schedule" button to see the latest schedule.
- Clicking the "Reserve" button will popup a message about your scheduling status.
- You are allowed to schedule several time slots, clicking "Done" button will quit the scheduling.
Gumbo provides a method for manually focusing the microscope by clicking the "Focus"tab:
- 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.
- 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.
- These buttons are used to real-time control the microscope:
Show Position: return your target to the microscope's current location.
Move: 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.
Refresh Video: refresh the video image. If you closed the Video Window, this button can bring it back.
Cancel Session: cancle your schedule to leave time to other users if you no longer control the microscope in the remaining time.
- Gumbo provides several different methods to focus the microscope. The "Quick"
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" uses a more reliable, but slower focus algorithm which samples the entire focal range before returning. If the "Quick" homes in on dirt or bubbles, you may want to use the "Accurate" to find the actual tissue.
- This group button allows you to move the slide step by step across the screen on 3 diamension bases, using the arrows for specific increments. This features is useful for cytology.
- Clicking on the "File" menu then selecting "New Session" will bring the starting window back.
Gumbo can display the stack distribution of your image acquisition jobs:
- Clicking the "Get Focus Stack" button 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.
Gumbo has been integrated with Mouse Brain Library and the application of Aria3D:
- The "Display User Job (or Display Library Stacks)" button will generate a list of your image acquisition jobs (or a list of Celloidin IDs that exist in our public library).
- If you select a particular job (or a slide), you can view the distribution of successful image stacks and null (or unsuccessful) image stacks.
- Gumbo automatically connects to Mouse Brain Library to retrieve the case information for the selected slide or job.
- Clicking the "Show Available Slide" button will bring the preview image of the slide currently available on the microsope to the corresponding window on the left.
- Clicking this button opens a message window indicating how to use this feature.
Gumbo can be used to create your own job, which can be viewed in Aria 3-D (IMPORTANT, WE RESERVE THE RIGHT TO INCLUDE YOUR JOB(S) (IMAGE STACKS) IN OUR PUBLIC LIBRARY AND REMOVE YOUR JOB FROM THE ISCOPE SERVER. Any comment please sends to Dr. Robert W. Williams ).
- Clicking "Link to MBL" button lauches the MBL browser to show the case information for the current slide.
- Clicking "Open Aria3D" button lauches Aria 3-D application that was developed by the iScope team at University of Tennessee Health Science Center.
Alignment between the preview images and the actual stage position is pretty darn important. Gumbo provides a function to allow the users to reset the calibration:
- Define a rectangular region to sample using "e;Set Top Left Corner"e; and "e;Set Bottom Right Corner"e;. Note that the "Set Top Left (or Bottom Right) Corner" button will become "Change Top Left (or Bottom Right) Corner" after you finish setting both corners, you can adjust the corners untill you satisfy your setting.
- Enter a job name and select a linear sample density. In order to prevent you messing up the other users' jobs, this version doesn't allow you to use a job name that has already existed in the iScope server.
- Clicking the "Create Job" button generates a message windows indicating that you will receive an email to be informed the status of your job when your job acquisition is completed. However, it will show the error message if your operation is incorrect.
- Click this button to reset selection.
- By checking "Filter Null Stacks", the iScope system will automatically filter null image stacks (e.g. tissue-like background) you may acquire and only send the meaningful acquisitions to the iscope server.
Now that you can obtain a focused image from the microscope, it is time to look at the options provided
in the Video window.
- It is easy to use this feature by following the instructions in the interface. We recommend you to move the microscope to the position with obvious features to facilitate your observation for the correct position.
- 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.
- The red box, which can be toggled by clicking the "Focus Overlay" radio button, selects
the region used for the focus stack discussed above.
- This comboBox allows you to display the different size of the video image.
- The X and Y box here show the current position of the red box in the video image.
- Entering the text in the lineEdit and clicking the "A" button generate a note in the video image in the disired position by clicking the right button of the mouse.
- Serveral image editing tools are provided here: line, rectangle, ellipse, draw, color, window size, eraser, zoom in, zoom out, selection, save all and save selection.
- A ruler is provided to show the size of the video image in pixel and um.
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,
Tony Capra or Senhua Yu.
I still use Gumbo old version.
November 13, 2003