Monday, April 21, 2008

Confocal -- mercury bulb alignment and field of view

On Friday, I had our service technician come to help figure out what was going on with a concern about the field of view. Essentially, a user has been looking at cells in the dentate gyrus of mouse sections -- granule cells specifically -- and finds that the field of view looks much larger than on the widefield fluorescence scope in his lab. This makes the cells look very small and harder to count, and images captured with the entire field of view don't "look right" because they seem zoomed out.
Earlier in the week, I had taken our calibration grid slide that I use to calibrate the Zeiss and we put it on the scope to see if there was any calibration issue. We were able to get an image of the calibration grid in the red channel and a granule cell in the green channel, and indeed the cell we were looking at appeared to be only about 5 um in diameter. The PI checked the literature and found these cells to generally be described as at least 10 um in diameter.

After much discussion with the rep, we concluded that indeed our confocal tends to have a larger default field of view than many other scopes, which can be reduced if desired using the Zoom or Crop feature of the Navigation menu. Talk to me if this is of concern to you or you'd like to learn more about it.

Later that day, we found that the mercury bulb was again out of alignment. This is the second or third time this has happened, and we are very puzzled as to how this could occur. I called our service technician back and asked him to come check it out, both to get it back in optimal alignment and see if he could find any reason for it to be going out of alignment without anyone intentionally touching the knobs. This mystery remains unsolved at the moment.

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