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FAQs

Details on how to book the Confocal Microscopy Unit can be found on the 'Booking' page.

Details on how to find the Confocal facility can be found on the 'Directions' page.

What laser lines does the confocal have? Details on what laser lines the Confocal has can be found on the 'Leica TCS' page.

Is the confocal microscope networked?

  • No, you will need to bring a portable USB storage device (e.g. flash drive) or CD-R/RW (but not DVD-R/RW) along with you.

Details on what fluorochromes to use can be found in the related resources section on the 'Leica TCS' page.

Details on the guidance notes needed for specimen preparation can be found on the 'Guidance' page.

Details on the tariff range for using the Confocal microscope can be found on the 'Charges' page.

Details on Confocal microscope user manuals can be found on the 'Leica TCS' page.

Details on how to obtain a copy of LCS Lite software can be found in the related links section on the 'Leica TCS' page.

How do I put a scalebar on my image in LCS Lite?

  1. Click on the Display Icon
  2. Choose Settings sub-menu
  3. Check tick box for Scale. A scale bar with dimensions in microns (to two decimal places) will be displayed in the bottom right hand corner of the image. You cannot change the scale bar value to a whole number – it requires the full version of the software, however this can easily be done in Adobe Photoshop.

How do I output my image files from LCS Lite?

  1. Right click on your image within LCS Lite and select Send To >
  2. You will have the option of sending to Experiment> or to Printer>. Select Experiment>. You will get 3 options: 1.selection (raw), 2. selection (snapshot), 3. all (snapshot).
  3. Choosing the first option will save the raw image (i.e. without scale bar, grid, annotations etc), choosing the second option will take a snapshot of the image delineated by the white dashed line, and choosing the third option will take a snapshot of the entire contents of the image display (viewer) window. These will be displayed in the file window of LCS Lite as either selection or snapshot.
  4. Rename these files by right clicking on them and then press the SAVE icon on the top bar of the control window to save them to hard disk

How do I overlay multiple fluorescent channels in LCS Lite to create a composite image?

  1. Click on the Ovl. (overlay) icon in LCS lite. This will create a new image displaying each of your fluorescent channels overlaid upon each other
  2. Right click on the overlaid image and repeat above procedure to output the new composite image.

How do I output animation sequences for presentation?

  1. Right click on the image files in the file window of LCS Lite and choose Export.
  2. Export as either .tiff or avi. formats.

N.B. you have the option of saving as .tiff or avi. files only with a section series. Single sections or projections can only be saved as avi. files using this method (the .avi file format is for movie animations and is recognised by Windows Media Player amongst other packages)

How do I view my exported animation sequences (.avi files)?

  1. Right click on your image file within My Computer (the file manager) on the Windows desktop,
  2. Select Open With from the menu that appears and select Windows Media Player. This will then open up your AVI. file within Windows Media Player

How do I incorporate my animation sequences (.avi files) into a Powerpoint presentation?

  1. Open PowerPoint and start a blank presentation
  2. From the top menu select Insert. When the sub-menu pops up select the double arrow at the bottom to expand the sub-menu options
  3. Select Movies & Sounds
  4. Select Movie from File
  5. Choose the AVI. file of interest .

The AVI. file will be inserted into PowerPoint and you will be prompted with the message "How do you want the movie to start in the slide show? (Automatically or When Clicked). Choose your preference.

How do I overlay selected sections from a stack using Adobe Photoshop?

  1. Open Adobe Photoshop. Select File > Open and highlight the images you wish to combine using the Ctrl key and press Open.
  2. Select Image > Image Size and note image dimensions (both pixel dimensions and document size)
  3. Select File > New and open a new image window of the same dimensions (above) as the original images you wish to merge in RGB colour.
  4. Select Window > Show Channels from the top menu.A new window will appear (if not present already) with the options Layers, Channels, Paths. Select the Channels option, then Select the Green channel
  5. Go the green image you wish to merge. Choose Select > All from the top menu, then choose Edit > Copy.
  6. Reselect the new image window and then select Edit > Paste
  7. Click off screen to deselect.
  8. Select the Red channel associated with the new image window.
  9. Go the red image you wish to merge. Choose Select > All from the top menu, then choose Edit > Copy.
  10. Reselect the new image window and then select Edit > Paste
  11. Click off screen to deselect.
  12. Select the blue channel and repeat the above procedure. If there is no blue channel image to be merged choose Select > All from the top menu, then choose Edit > Fill. A Fill window should now appear – use Black as the fill colour.
  13. Select the RGB channel and you will now see the merged image. Save as RBG merged image.

 

Page content written and maintained by Dr. A.J. Hayes and Mr. M. Isaacs