PerkinElmer Spotlight 200, User Manual

Page: 107 / 132

Techniques for Collecting Spectra . 107
To scan a marker:
1. Select
Microscope
>
Stage Move
>
To Coordinate
and enter the coordinates for the
marker you selected in step 16 multiplied by the correction factor.
Refer to
Correcting the Coordinates of Markers
on page 107. The stage will move to the
correct position.
2. Click to scan the marker.
3. Repeat as necessary for other markers.
To scan lines or maps:

Click to collect all the required spectra automatically.
Correcting for the Effect of the ATR Crystal
It is very important to correct for the optical effects of the ATR crystal when selecting areas
of the sample to analyze, and when setting the aperture dimensions. These effects arise
because the refractive index of the crystal is much higher than that of air, which causes the
sample image to be magnified when the crystal is in place. Therefore, the distances seen on
the image survey, which was collected when passing the beam through air, will be different
when the beam passes through the ATR crystal.
The ATR crystal is made of germanium, which has a refractive index of 4.0.
Adjusting the Aperture Sizes
The crystal’s refractive index causes the actual area scanned on the sample to be smaller
than the selected aperture area.
1. Select aperture sizes on the image survey to include the features you want to scan.
2. Increase the aperture sizes by a correction factor in both the X and Y directions to make
sure that the scan covers the equivalent area that you originally selected in the image
survey.
For germanium, the correction factor is 4.
Correcting the Coordinates of Markers
The coordinates of markers on the image survey will not relate to the same position on the
magnified image produced by the ATR crystal. A correction must be applied for each marker.
For this reason, we recommend that you only use the following procedure to scan markers
with Spectrum software:
1. Note the coordinates of the point you want to scan in your image survey.
These coordinates must be based on the origin of the stage being set at the center of
the crystal.
2. Multiply the X and Y coordinates by a correction factor.
For germanium, the correction factor is 4.