D1 Sample Microscope

Detlef Smilgies, CHESS

Introduction

The D1 microscope consists of a Navitar motorized zoom and focus module with on-axis lighting, as well as several front lenses (0.5x, 0.75x, 1x = no lens, 2x) as well as 2 tubes (1x, 2x). Images are collected by streaming video from the SONY CCD camera. The system is controlled by the Crystal Centering program developed in the MacCHESS group (Richard Gillilan, Dave Schuller).

Note: Most of the features of the centering software on the bottom control bar features are currently not used (the spindle rotation is only for crystallography, the sample x and z translations are currently only supported within SPEC.)

Cabling & re-activation

Most of the cabling is already done and componets are kept in the D1 hutch crate.

connect serial port cable of focus/zoom controller to centering computer
connect firewire cable of Sony camera to centering computer
connect power supply of focus/zoom controller
connect power supply of on-axis lighting controller
microscope and camera unit should be already wired (focus, zoom, on-axis lighting)

For re-activation of the centering system (for instance after CESR-TA run):

start centering computer
switch on zfocus/zoom controller
switch on lighting controller - make sure that light is not set too bright

Starting and using the CrystalCentering program

On the Linux PC go to the /CrystalCentering directory and type center_server to start the program.
use the "Zoom" tab to adjust Zoom (with the slider) and Focus (type value in the box or use the arrows)

note: check with beamline staff whether the microscope is set up to track properly

use the "Cam" tab to adjust the brightness and color of the image

"Brightness" uses the computer software to brighten images
"Gain" is the gain of the CCD camera to brighten images
"Shutter Speed" controls the exposure of the camera to brighten images

if Speed is set too slow, images will be blurry when the sample moves

"White Bal UB" and "White Bal VR" affect the color of the images
the on-axis lighting currently cannot be controlled remotely - use the manual control box in the hutch

"Save Photos" in the top menu bar enables saving of microscope images

only the "single snap" option is currently supported

"Visual Aids" in the top menu bar toggles the crosshair and the scale bar on and off
"Admin Only" in the top menu bar enables line-up features

"Set Crosshair" plus doubeclick moves the crosshair to a new location
"Midpoint Tool" determines the center between 2 spots vertically (doubleclick on each spot)

Calibrating the microscope

NOTE: this part is for beamline staff and expert users only

The CrystalCentering program, as used at D1, has 5 calibration parameters which are found in conf/server.properties.
When changing a value, the program needs to be restarted.

zcenX, zcenY or the coordinates of the invariant point under zoom
beamDiameter defines the diameter of the crosshair circle in microns
zoomSlope and zoomIntercept are used to calibrate the onscreen pixels to microns

Calibration procedures

pixel coordinates and zoom and focus values

on the main directory type "tail -f center.log" - this will provide zoom, and focus values as well as the pixel position of the crosshair when you use the midpoint tool
(the "tail" command displays the last 20 lines of the logfile and updates automatically)

finding the invariant point (R. Gillilan)

using a test object on the xyz sample stage find a sharp feature, such as the tip of a needle
estimate the invariant point from the previous position of simply the center of the screen
zoom in and put the needle tip into the crosshair
zoom out and move the crosshair to the needle tip
iterate step 3 and 4 until the crosshair remains on the needle tip for all zoom values
update zcenX and zcenY and restart the centering program.

note: this procedure needs to be repeated, whenever the microscope is remounted, or lenses, tubes or cameras have been changed

calibration (R. Gillilan)

zoomSlope and zooIntercept are determined in a graph log(pixels/micron) versus zoom units
use a calibrated test grid for calibration (R. Gillilan has an electron microscope scale which works great)
if the the in-line mirror is used the calibration needs to be done both in x and z. samth should be aligned such that the x and z values for pixels/micron agree
for every change of the optics the microscope needs to be recalibtrated.