This chapter describes the adjustment procedure to
reach perpendicularity between the objective (optical axis) and the slide
surface (specimen holder).
Because this adjustment needs special tools and might
be time consuming, it should not be done in the field; an experienced
technician may execute these steps in the service center.
The adjustment is based on the software version 1.15
and the scanner P250, but the principle and almost all procedures are the same
in the scanners S_M_D.
Adjust the parallelogram
Prepare the scanner for the adjustment
Images of the adjustment steps
The optical axis of the objective and the glass slide
needs to be perpendicular to avoid tilting and partially out of focus FOVs on
digital slides.
As commonly known, in Pannoramic
scanners, the slide is moved with the focus pin around the nominal focus
position (around the position +500 steps; in S_M_D this position is 1600 steps
nominal) during focusing. To shift the slide in the Z-direction (this means
focusing) and not inclining or tilting the slide during these movements, a
parallelogram is used; the parallelogram is mounted between the Y-carriage and
the specimen holder.
Also important is the position of the parallelogram in
relation to the X-plane and the Y-plane of the slide.
Best scanning results will be reached if the slide is
perpendicular to the optical axis.
·
The adjustment,
described in this chapter, defines the position of the parallelogram so, that
the inclination of the slide in the X-Z-plane and the Y-Z-plane will not exceed
the allowed limits.
More information can also be found in the chapters:
· “Focus unit” and “Scan area”, “Principle of
focusing”
· “X-Y-Stage unit”, “Parallelogram” , “Specimen holder”
· “Optics and illumination”, “Stage skew
check”
Ideal position of the slide in the
specimen holder
In the ideal position of the slide, the optical axis is
perpendicular to the slide surface and by moving the focus pin in the range of
-300 steps to +1300 steps or by selecting any field of view inside the scan
area, this perpendicularity will not be lost; the LASER beam (reflected by the
slide surface) would be always reflected in the same angle onto the same
position of the screen during movements of the slide.
1) The ideal slide position would be reached if the field
of view (FOV), near to the limit Y-min would be in the same plane as the field
of view near to the position Y-max (shown with the line (Y))
And
2) The field of view, near to the limit X-min would be in
the same plane as the field of view near to the position X-max (shown with the
line (X)).
·
If this
requirement is fulfilled, the optical axis is perpendicular to the slide
surface.
This definition
assumes also:
·
The slide (the
glass) itself is flat, and not tilted or slant in any direction and the slide
thickness does not vary.
·
The force of
the preload spring of the parallelogram is not much; otherwise, the pressure of
the focus pin against the slide may tilt the slide surface in positions of the
field of view, far away from the holding mechanics (c).
In practice, the ideal position will not be reached, but
the inclination of the slide in X- and Y-direction may be reduced as much as
possible.
·
The slide will
be inclined in the X-Z-plane, in the Y-Z-plane or in both planes at the same
time, but always inside the allowed tolerances.
·
In these cases,
the Z-axis of the slide will be inclined, in relation to the optical axis.
The LASER beam will be reflected to a different
position onto the screen (in relation to the ideal position of the slide).
·
The inclination
of the slide may result in unfocused parts of the virtual slide and these are
best visible on the border of the actual field of view in relation to the
neighbor FOV, if the inclination of any plane is too much.
Faulty inclination of the slide in the specimen holder
The real position of the slide is faulty if:
·
The Z-axis of
the slide is inclined, in relation to the optical axis; outside the allowed
limits.
The inclination angle of the slide’s X-Z- or
Y-Z-plane is too much, if the focus of the field of view differs (the focus
difference is visible) on the border to the neighbor field of view in the
virtual tissue and:
·
The slide is
correctly inserted into the specimen holder
·
The slide is
held properly in the specimen holder (the slide does not change its position
during scanning)
·
This behavior
can be detected often on two neighbor FOV’s on different positions of the
scanned tissue; the border of the FOV is visible (in relation to the focus).
·
The neighboring
FOV’s are scanned in the same focus motor step position
·
Some parts of
the field of view are out of focus while other parts of the same field of view
are in focus
·
This behavior
can be found on different tissues (slides) also.
·
By adjusting
the parallelogram position, the inclination of the slide in relation to the
optical axis will be minimized or eliminated; this is the task of the
adjustment.
Remark
·
During the tissue creation process the
thickness of the sample itself may vary on small spots and this might also be
visible as unfocused part of the virtual tissue. To decide, whether the
thickness of the sample is varying or the inclination of the slide is the cause
of the error, please check always the focus on the border of the FOV in
relation to its neighbor FOV on different tissues also.
·
The inclination of the specimen (holder)
may also be checked in the live view and with a zoom factor of 2.73 of the scan
program; see also: “Stage skew check”.
In all cases
If the scanned tissue shows mistakes or errors, that
may occur in conjunction with non perpendicularity of the objective (Optical
axis) and the specimen holder (slide surface) (some parts of the field of view
are out of focus during other parts of the same field of view are in focus) and
this behavior can be detected very often on two neighbor FOV’s and there is no
difference in focus steps, the following checks have to be done first:
Please do the following
checks before you set up the adjustment tools!
Any mechanical reason or incorrectness named above may
result in the incorrectness of the optical axis; if one component is not placed
well in the optical axis, the result is the same as if the parallelogram would
be adjusted wrong!!
When shell I check or adjust the parallelism between
the focus- and the X-Y-stage unit?
To
check the parallelism, use always the “Stage skew check” first, before you set up the adjustment tools!
Attention
If the parallelogram or the specimen holder is deformed (bent) or any
spring of the parallelogram is broken or deformed, this adjustment will not
deliver the desired results!
Exchange
the appropriate spare part first before doing the adjustment steps.
Important
If
any modification on the parallelogram or the specimen holder mounting was done,
please:
·
Check or adjust the magazine unit position.
·
Check or adjust the correct position of the specimen holder fixing fork.
· Check or define the
scan area again before scanning tissues!
· If the scan area was modified, please execute the preview calibration also.
· Check the darkfield preview.
Requirements
·
The tools, described in the chapter “Tools used for the
adjustment”.
·
Diverse hexagon key bolt drivers
·
Service program “SlideScannerService.exe”
·
Scan program (SlideScanner.exe)
·
Viewer program (“SlideViewer.exe”)
·
Required time may be 2 hours or more.
Remark
The
required time depends highly on the misalignment of the parallelogram, the post
adjustments and checks that has to be done (see above “Important”) and,
nevertheless, the experience of the technician.
The
target is placed in a nominal distance of about 3m to 3.5m from the scanner
onto the wall and is used as a screen.
The
marker areas on it are used to check the adjustment result.
The
momentarily adjustment is qualified nearly in the center of the scan area and
in the focus positions:
-300
steps +500 steps and +1300 steps
If
the travel of the LASER beam does not go out of the green area during the focus
movements (if the distance is in the range between 3m - 3.5m), you have shot
the bull’s eye.
If
the distance is shorter than 3meters (e.g. only 2.5m) the allowed movements
should be closer to the black circle in the center; the acceptable (green) area
has to be defined smaller.
For
best adjustment results a distance of at least 3m is recommended; further
details will be discussed later.
· You may also create
and print your own target by the help of any
image editor that is able to draw circles or print the example target.
LASER source
holder with beam mirror
As light source of the LASER beam a LASER pointer or any other kind of
LASER source can be used; the mechanical construction may be important for the
mounting possibilities.
Precautions
Never look directly into the LASER beam of the LASER source!
The emitted LASER beam has only a power of about 0.01watts but this is enough
to damage the retina of the eye!
The mirror is mounted at an angle of 45º
onto the LASER source holder and may be used to reflect the beam sideways, onto
the wall.
The
LASER source holder can be mounted so, that the beam passes the opposite side
(or any side) of the LASER source mounting where no mirror is mounted.
·
See also: “Arrangement 1”
Into the “objective position
· If the objective position is already adjusted please do not loosen the
objective nut (or the objective counter nut) during removing the objective;
otherwise the adjusted objective position will be lost!
This
mirror defines the plane of the objective pupil; the mirror is mounted
perpendicular to the optical axis and is used to arrange the entire
configuration for the real adjustment.
After
the configuration is arranged, this mirror is not needed for the real
adjustment.
See
also “Arrangement 1” and “Arrangement 2”.
Remark
·
Because the plane of the objective pupil
has to be checked more times during the adjustment, we recommend to remove both
objectives (the 20x and the 40x objective or the dummy objective also).
· By rotating the objective disc manually into the objective position 1 or
2 respectively, you can easily and quickly “switch” between the
“Arrangement 1” and the “Arrangement 2”.
Another
solution
A simple mirror may also be used to define the objective plane, instead
of the objective mirror; see also “Arrangement
Dismount
the objective by unscrewing only the objective from the objective nut; do not
modify the adjusted objective position (the wrenches should not be used).
Important
The
actual reference surface position should be checked more times during the
adjustment process.
To
mount the LASER source in the correct position over the focus unit, this
holding system is used; the dovetail foot is mounted onto the truss, onto the
position of the turret unit fixing clamp. Onto the other end of the holding
system the LASER source holder fixing with mirror is mounted.
· You can also use any holding system that allows the position adjustment
of the LASER source holder with mirror in the X-, Y- and Z-direction of the
room co-ordinates.
See
also: Holding systems from NOGA “http://www.noga.com/”
The mirror slide is used in the “Arrangement 2”; it deflects
the LASER beam according to the inclination of the specimen holder; the angle
of the inclination is added to the angle of the LASER beam and so the LASER
beam is deflected more, less or equal in relation to the “Arrangement 1”.
Remark
The
LASER beam will be reflected on the surface of a simple slide also; so it is
not important to use a mirror slide in the arrangement 2; but the description
refers always to “the mirror slide”!
·
Please check the shape and the surface of
the no-coated slide carefully before using it during the adjustment!
This component ensures the parallel shifting of the X-Y plane if the
focus pin moves the slide toward or away from the objective (in Z-direction).
·
The position of the component in relation
to the X-Y-plane of the slide defines the perpendicularity of the optical axis
in relation to the slide surface (tissue).
For
working principle, please see: Parallelogram
The connection surfaces to the Y-carriage and the specimen holder are
grinded to ensure the parallelism of both connected components.
Parallelogram
movement limiter
The allowed movement of the parallelogram is limited to be 0.8 mm
over all (in opposite to S_M_D = 0.5mm). This limit is constant and can not be adjusted separately. To adjust the correct
limiter position a fitting plate is used. The thickness of the used fitting
plate defines the correct position of the entire parallelogram and so the
position of the parallelogram axle in relation to the limiter also.
How to check the acting range of the
parallelogram and the movement limiter?
1) Move the stage with the service program nearly into the middle of the
scan area.
2) Set the focus motor to Home 1,2
3) Set the focus motor to the position -300 steps.
4) Check the position of the parallelogram axle in relation to the limiter;
in this position a small gap should exist and the focus pin should be in
connection to the slide.
5) Set the focus motor to the position +1300 steps.
6) Check the position of the parallelogram axle in relation to the limiter;
in this position a small gap should also exist.
·
If a small gap on both limit positions can
be found, the focus pin is always in connection with the slide and the
inclination angle adjustment of the slide is finished (the adjustment of the
parallelogram position), the movement limit of the parallelogram is well
defined.
·
During the adjustment procedure of the
parallelogram position please check this behavior more times; even if the
inclination angle of the slide in X-direction was modified!
·
If there is no gap in the appropriate
limit position or the slide is not in connection with the slide over the entire
focus range, the inclination of the slide in X-direction may be wrong or the
thickness of the fitting plate may be selected incorrectly.
The preload spring is used to create a force of the specimen holder
against the focus pin, so a mechanical preload is created. With this solution the slide is
always in connection with the focus pin during focusing or specimen holder
movements in the scan process.
Before you mount the parallelogram (even if a used one should be
mounted) you have to check it of functionality, visually. The parallelogram is
correct if all 8 mounting spring leafs are not bent or broken. The flat springs
are the most sensitive parts of the parallelogram.
· Compare the look of the springs to each other!
The fitting plate is used to define the parallelogram limiter so, that
the limiter does not limit the parallelogram movement in the range between -300
and +1300 focus steps; the thickness of the selected fitting plate is correct
if there a small gap on the limiter exists if the focus position of -300 steps
is reached and even so, there have also to be a small gap if the focus position
of +1300 steps is reached.
· The fitting plate is mounted between the
Y-carriage and the parallelogram.
· The drillings and edges have to be burred;
the surface should be smooth.
· The nominal thickness of the fitting plate can be 0.1 mm, 0.2
mm, 0.3 mm, 0.4 mm, 0.5 mm or any combination of two
fitting plates.
· The thickness of the fitting plate is often
found between 0 (no fitting plate used) and 0.5 mm.
· The fitting plate has to cover the entire
mounting surface of the parallelogram; see also below “Mount the parallelogram”.
· In exceptions, the fitting plate might be mounted between the specimen
holder and the parallelogram (if a negative value for the fitting plate
thickness have to be reached); in this cases, there have not to be a fitting
plate on the mounting surface between parallelogram and Y-carriage; the
adjustment bolt(s) are always used on the side, where the fitting plate is
placed.
Inclination
angle adjustment in X-direction
This adjustment bolt is used to define the angle of the parallelogram
and so the angle of the specimen holder (slide). By screwing the X-direction
preload angle bolt, the inclination angle of the parallelogram can be adjusted
to zero (the angle of inclination between X-min and X-max of the scan area).
IMPORTANT: The limit of the parallelogram movement limiter is affected also and has
to be checked always after driving the bolt.
See
also: “How
to check the acting range of the parallelogram”
Inclination angle adjustment in Y-direction
With this adjustment the angle of inclination in Y-direction is reduced
/ eliminated; it means the inclination angle between Y-min and Y-max of the scan area.
· By loosening the mounting bolt and
tightening the adjustment bolt or by loosening the adjustment bolt and
tightening the mounting bolt, the angle of the inclination in Y-direction is
modified.
· The adjustment is done only on one side; the
adjustment bolt of the opposite side should be fully loosened (or removed)!
· If the adjustment on the actual side does
not deliver the desired result, change the adjustment bolt to the opposite side
and execute the adjustment there.
On this side the parallelogram is mounted together with the fitting
plate (if needed).
· Place the fitting plate so, that the entire (grinded) mounting surface
of the parallelogram is covered by the fitting plate.
· If the thickness of the fitting plate has to
be modified, dismount the entire parallelogram with specimen holder, exchange
the fitting plate and mount the parallelogram again (the two mounting bolts).
On
the opposite side of the parallelogram the specimen holder is mounted, usually
without fitting plate and without adjustment bolts.
In
exceptions, the fitting plate is mounted between the specimen holder and the
parallelogram (if a negative value for the fitting plate thickness have to be
reached); in this cases, there have not to be a fitting plate on the mounting
surface between parallelogram and Y-carriage; the adjustment bolt(s) are always
used on the side, where the fitting plate is placed.
In “Arrangement 1” the position of the entire scanner, more
precise, the position of the objective nut will be defined; in
“Arrangement 2” the position of the specimen holder in relation to
the previous arrangement will be defined. In other words, the plane defined by
the objective mirror is used as reference plane and the plane of the specimen
holder with the mirror slide will be adjusted to the reference plane. Therefore
it is important, that the found position of the reference plane during the
“Arrangement
This
means:
·
The positions of the components must not
be altered until proper alignment is reached.
Please do
not move
·
The table
·
The entire scanner or the truss
·
The holding system (it may occur if the
parallelogram bolts are driven)
·
The LASER source (it may occur if the
parallelogram bolts are driven) and
·
The screen until the entire adjustment is
not finished correctly.
If
one of the named components changed its position, please rotate or insert the
objective mirror into the optical axis again, remove the target and stick it
again onto the wall in the right beam position; or start with “Arrangement
Change the objective to the objective mirror.
Mount
the LASER source holder with the holding system over the objective nut.
Adjust
the position of the laser source holder so, that the LASER beam is reflected by
the objective mirror to the LASER beam mirror in an angle that is nearly
perpendicular.
The
angle of the laser beam, reflected by the objective mirror should be as small
as possible; so the error of the adjustment will be small also.
·
To reach this, the LASER beam source holder should be mounted
at a large distance from the objective nut.
By
positioning the entire scanner and the holding system find a well reachable and
visible part on the wall (use the LASER beam) and stick the screen onto the
wall with the LASER beam in the center of the marker position.
Arrangement 1B
The only difference to the arrangement 1A is the use of the LASER beam
mirror.
·
In the arrangement 1B the LASER beam
mirror is not used.
See
also: Known
errors
·
Important: The
LASER
beam source holder should be mounted at a large distance to the objective nut.
Arrangement
·
The LASER beam mirror may be used or not like shown in the arrangement
1A or 1B.
·
The main difference to the arrangement 1A
or 1B is the use of a “simple mirror” on the objective nut instead of the
objective mirror.
This
version needs more accuracy during the preparation of the adjustment
See
also: Known
errors
·
Important: The
LASER
beam source holder should be mounted at a large distance to the objective nut.
Arrangement
2A
Rotate the objective disc into the objective position 2 (there is no
objective present).
If
arrangement
See
also: Known
errors
Insert the mirror slide (manually); the LASER beam should be visible on the screen again.
With
the X-Y-stage tools of the service program find a position for the specimen
holder nearly in the middle of the mirror slide’s scan area.
Set
the focus position with the service program to -300 steps and +1300 steps and
check the movement of the LASER beam on the screen several times.
Arrangement
2B
The only difference from arrangement 2A is the use of the LASER beam
mirror; depending on the used arrangement 1.
·
In the arrangement 2B the LASER beam
mirror is not used.
See
also: Known
errors
The mirror position difference between the mirror slide and the
objective mirror in the arrangement 1 and 2 contains automatically a
measurement error.
·
To reduce adjustment errors, the angle of
the LASER beam should be as close to perpendicular as possible!
·
To reach an angle of the LASER beam close
to perpendicular, the LASER source holder should be mounted far away from the objective nut as
much as possible and the reflected LASER beam should pass the LASER source as
close as possible.
Arrangement 1A or 1B
If
the objective mirror is used, the angle is always close to perpendicular (very
small), because the mirror surface is small and the LASER beam is routed in a tube.
Arrangement
To
minimize the error of the adjustment, the angle of the LASER beam should be
close to perpendicular and should match the illumination hole of the focusing
part.
·
Arrange the position of the LASER source
precise with a very small angle!
Because
a simple mirror is used on the objective mounting nut, the distance of the simple mirror to the
mirror slide is more than in the arrangement 1A or 1B; there is no tube part used to route the LASER beam and the mirroring surface of the simple mirror
is large; the error of the adjustment will also be more.
Please take all this into account if the
tools will be arranged!
Prepare the scanner for the adjustment
1) Remove the upper housing cover.
3) Remove
the entire preview unit
4) Set the working position of the objective changer unit
to the objective position 1.
5) Remove the objective changer drive unit.
6) Dismount the 20x objective.
7) Mount the objective mirror.
8) Dismount the 40x or the dummy objective.
9) Mount the holding system onto the truss, use the mounting bolts of the upper clamp and tighten
the dovetail foot.
10) Mount the LASER source holder with LASER source as shown in the “Arrangement 1A or 1B”; see also Known
errors
11) By positioning the entire scanner find a well reachable / visible part
on the wall (use the LASER beam) and stick the screen onto the wall with the
LASER beam in the center of the marker position.
12) If the position is found as desired and the screen is stuck onto the
wall the “Arrangement 1” is finished.
·
If the screen is stuck onto the wall the
entire arrangement position must not be altered until the entire adjustment is
finished; see also The principle of the adjustment.
·
If one of the used components changed its
position, please rotate / insert the objective mirror again into the optical
axis and check / adjust the “Arrangement 1” again.
13) Rotate the objective disc into the objective position 2 manually.
14) If the arrangement
15) Insert the mirror slide (manually); the LASER beam should be visible on
the screen again; see also: “Images of the adjustment steps”.
16) With the X-Y-stage tools of the service program find a position for the
specimen holder nearly in the middle of the mirror slide’s scan area.
17) Set the focus position with the service program to -300 steps and +1300
steps more times and check the movement of the laser beam on the screen.
18) Set the focus position to -300 steps.
19)
Adjust the parallelogram limiter position
by selecting the appropriate thickness of the
fitting plate (if required).
20)
Check the behavior of the parallelogram movement
limiter.
21)
Incline the mirror slide in Y-direction so, that the LASER beam moves in direction to the center of the target.
22)
Check the momentarily adjustment.
23) Set the focus position to +500 steps.
24) Repeat the previous 3 steps until the inclining of the mirror slide in
Y-direction will not improve the result.
25) Check the “Arrangement 1”
26) Incline the mirror slide in X-direction so, that the LASER beam moves in direction to the center of the target.
27)
Check the momentarily adjustment.
28)
In the focus positions -300 steps and
+1300 steps check the gaps of the movement limiter.
29) Set the focus position to +500 steps.
30) Repeat the steps from step 21 until only a movement inside the limits of
the target can be expired.
31) Check the “Arrangement 1”
32) Check the momentarily adjustment.
33) Check the entire adjustment near to the limits of the scan area; see
also: “Images of the adjustment steps”
34) Check the behavior of the parallelogram movement
limiter.
35) Check the “Arrangement 1”
36) Move the stage to the center of the scan area and check the movement of
the LASER beam on the target in the focus positions -300 steps, +500 steps and
+1300 steps.
37) Check the behavior (acting range) of the parallelogram
movement limiter.
38) Check the entire adjustment near to the limits of the scan area; see also: “Images of the adjustment steps”
·
If the movement of the LASER beam on the
target is inside the limits in the named positions, the adjustment is finished
and the scanner can be assembled.
39) Mount the objectives.
40) Mount the objective changer drive unit.
43) Check / adjust the position of the magazine unit.
44) Check / adjust the correct position of the specimen holder fixing fork.
45) Check / adjust the objective position
46) Check / define the
scan area
47) If the scan area was modified, please execute the preview calibration also.
48) Check / adjust the darkfield
preview.
Check the momentarily adjustment
Move
the stage near to the center of the scan area and check the beam behavior on
the target in the focus positions
-300
focus steps +500 focus
steps and +1300 focus steps.
The
LASER beam should move only a little bit.
·
Check the behavior of the parallelogram movement
limiter
Check the behavior of the parallelogram movement
limiter
·
In the positions -300 focus steps and
+1300 steps please check the limit of the parallelogram limiter; a small gap
should exist.
·
In the position -300 focus steps please
check the connection of the slide with the focus pin; the focus pin should
touch the slide.
If
any requirement is not fulfilled, select the correct thickness of the
fitting plate.
Incline the slide in X-direction
Move
the stage nearly into the center of the scan area.
Set
the focus motor to the position +500 steps.
Drive
the X-direction preload angle bolt carefully in the appropriate direction; the
beam should move in direction to the center of the marker circles.
Check the behavior of the parallelogram movement
limiter
Incline the slide in Y-direction
Move
the stage nearly into the center of the scan area .
Set
the focus motor to the position +500 steps.
Modify the position of the parallelogram in
Y-direction; the beam should move in direction to the
center of the marker circles.
Dismount
the objective and mount the objective mirror
1. With the program SlideScannerService.exe set
the X-Y-stage to the positions Y-Home1,2 and
X-Home1,2.
2. In
the tab “Objective changer” move the objective (position), to be dismounted or
mounted into the working position.
3. Select
the option “Time out”, set a numerical value of about 1000ms and press the
button Backward.
4. Dismount
/ mount the objective (mirror). Hold the mounting nut with the delivered wrench
and remove / mount the objective (mirror) by hand.
·
Please do not modify the objective nut position;
otherwise, the adjusted focus position will be lost!
5. Select
the appropriate sensor and press the button forward; the actual dismounted
position or the mounted objective should move into the working position.
6. Repeat
the steps 2 to 5 with the other objective (position), if necessary.
7. If
the 40x objective was mounted, check / select the thickness of the cover slip;
see also “The 40x objective”.
Images of the adjustment steps; P250
The
LASER beam is shown after sticking the screen onto the wall (after finishing the arrangement 1).
·
The distance of the screen to the
scanner’s objective nut is ~4.8m.
The
mirror slide is inserted; the LASER beam is shown first time with the mirror
slide; nearly in the center of the scan area.
Images of the adjustment steps; SCAN
Objective mirror and arrangement 1
Arrangement 2; objective nut with mirror removed
Adjustment results; SCAN
The distance between scanner and wall is 3.10m; the pictures are taken
nearly in the middle of the scan area.
·
Check the adjustment with the stage skew
check; see “Stage skew check”
·
Check the scan area; see “Scan area”, and check the preview in SlideScanner.exe or execute the preview calibration
respectively, if required!