Taking snapshots with Noran confocal software

Converting Noran files to snapshots (TIFF or GIF images):

1. Take your image using normal methods: for a 2D image, you probably want medium resolution, perhaps with some jump averaging to improve the image quality. You want to take 1 image (not a sequence) usually, although the methods below will work to grab some pictures from a sequence of images.

2. On the SGI computer, under the Toolchest, go to Intervision-->2D Analysis to start the 2D Analysis program.

3. In that program, go to File-->Open and load in your data file

4. You want to make the image pretty:

   View-->Display Color Bar (turn option off) View-->Annotation (set style to Helvetica, set Small Font to Large Font in both places, hit Dismiss -- see image at right View-->Display Scale Bar (turn option on) If you don't like the scale bar, use the Annotation window to change its location, color, etc.

5. If you want, you can change the brightness and contrast, or zoom by using the two icons at the upper left of the 2D Analysis window. See picture at right.

   Brightness/Contrast: Click on the left one, put your mouse over the image, hold left mouse button down, move up or down to change contrast, move left or right to change brightness. Right-click to restore to original quality. Zoom: Click the 2nd icon from left, use left mouse button to pan, middle mouse button to zoom, similar to acquiring data. Right-click to restore original pan/zoom settings.

   Brightness/Contrast Pan/Zoom

6. Save the image using: File-->Snapshot.

   Change SGI RGB to TIFF-8 bit The image will be saved with the name snapshot0.tif unless you change it. A limitation is that you always have a string and a number (in other words blah57.tif is OK but blah.tif won't work). However you can change both the string and the number. NOTE: Do not save image using "Save As." This does not create a TIFF file.

7. Transfer the image to a Linux computer (ie pizza.physics.emory.edu), using ftp from pizza:
   • pizza% ftp epoxy
   • ftp> mget *.tif
   • ftp> bye

8. When done, exit 2D analysis: File-->Exit. It will tell you that you have changed your data and ask you if you want to save the changes; click "Don't Save".

9. On your Linux computer: use "xv" to convert to GIF:
   • xv blah57.tif
   • right-click on image, this calls up xv menu
   • click Save, change file format to GIF
   • can also use "xv" to modify appearance of figure, crop the image, resize it, etc. (I used "xv" to create the small images on this web page... click them to see original size.)
   • Type "e" within xv to edit the color palette

10. Note that you can use the "3D Analysis" program on the SGI computer to prepare 3D snapshots.

Notes:

• Warning: The scale bar is set based on information saved with your Noran file, including the objective you were using and the zoom. If you forgot to set the proper objective before you took the picture, the scale bar will be incorrect. Zooming is handled properly, though (the scale bar is the correct size if you were using zoom when you took the picture).
• You can find out more about the 2D Analysis program in the Oz/Intervision manual, Chapter 5 or 6 (Chapter 6 repeats Chapter 5 in more detail.)
• Image of particles at right: large fluorescent particles prepared by Martin Frank, picture taken by Martin & Eric Weeks. Image cropped using "xv".