Microarrayer Calibration | Online Docs

System Calibration

LabNEXT microarrayers are shipped pre-calibrated. Normally calibration is not required to start operations.
However in the course of operations incidental misalignments occur and need to be adjusted.
Complete system calibration is necessary only if a major change in the work board components and print
head takes place.

Making Small Adjustments

There is no need to run through the complete ( and lengthy ) process of system calibration in order to adjust
position of the pin in the washer/dryer station, source plate or change hight the pin travels over the slide
holders. Such a small adjustment can be done by slightly changing small values of the variables responsible
for the corresponding position or parameter.

All parameters are accessible via the ConfigureSystem utility.
Use the link for complete reference of the system parameters.

NOTE: The microarrayer must be connected to the USB port of the PC to run ConfigureSystem.
There is no need to perform "Home" operation as all adjustments are done manually.
If you manually change the value of a parameter that has "Register" button next to it, do NOT click "Register".
Simply enter a new value in the edit fields and click "Save" button at the bottom of the dialog window.

Example of Adjusting Dryer Position

In this example the pin misses center of the hole 0.3mm to the left, 0.2 to the front and goes 0.5 higher
desired depth in the dryer hole.
We need to adjust position of the pin in the dryer hole. ( Make it go right 0.3mm, back 0.2mm and lower 0.5mm)

1. Connect the Microarrayer to the USB port.
2. Run "Configure System"

3. Change the following parameters (refer to the Configure System online docs to locate them):

dryerX - increase current value 0.3 (this will make the pin go to the right).
old value= 105.1,
new value = 105.4
dryerY - decrease current value 0.2 (decrease will make the pin go towards back of the workboard)
old value = 71.8,
new value = 71.6

dryerHeight - increase current value 0.5 ( this will make the pin goes deeper)
old value = -10.5
new value = -10.2

NOTE: Values may be negative and -1 is bigger than -2.

Enter the necessary values. ( Do not click "Register" button )

4. Click "Save" button at the bottom of the "Work Board Editor Dialog".

5. Run a print job that uses just edited WorkBoard settings to see it the adjustment was sufficient.

Direction of Adjustments

In general for all geometry related variables in the system the following value changes result in the following
adjustments:

Z increase results in lower movement ( 5 is deeper than 4; -3.5 is deeper than -4.5 )

Y increase results in movement towards the front ( 12 is closer than 11 )

X increase results in movement towards the right side ( 23 is more to the right then 20 )

Changing Values via the File System

If for some reason the microarrayer can not be connected to the USB port, there is a way of editing system
settings directly in the file where they are stored.
The settings are stored in a plain text files, that can be opened and edited by any text editor, such as
Windows "Text Pad".
NOTE: The file names have no extensions, never the lees they can be opened by a text editor.

Most of the settings related to the microarrayer calibration are in the c:/labnext/PRODUCTION_DATA/workboard
folder. Name of each file is equal to the name of the work board, visible in the ConfigureSystem utility.
The data inside the file have the following format:

>>>
.....
dryerX: 251.0;
dryerY: -7.4;
dryerHeight: 34.4;
washerX0: 276.428894531;
washerY0: -7.4;
washerX1: 276.428894531;
washerY1: -7.4;
washerHeight: 36.5;
overSlideNestHeight: 33.98952375;

>>>

Names of the variables are identical to the names shown in the ConfigureSystem.
Editing the numerical values (and saving changes in the file) has the same effect as editing settings in the
ConfigureSystem ( and clicking "Save" button at the bottom of the dialog ).

The the ConfigureSystem utility online manual includes "File system location"
sections for each group of the system settings.

NOTE: If a misalignment occurs, it is an indication that some part of the system has shifted. For example the
head holder was hit by hand and moved in its mounting or the head holding screws became loose.

We recommend making a quick assessment of the cause of the misalignment before proceeding with system settings
adjustments. If there is a loose part, fix it properly and then adjust the settings. ( Otherwise the misalignment
will keep happening again ).

Some misalignments occur due to the difference in labware size. If you install a new type of the source plate or
microarray slide their dimensions can slightly differ from the ones used previously.
In this case we recommend registering new plate or substrate instead of making adjustments in the WorkBoard
configuration.

Please refer to the JobWizard utility online docs as the labware is registered
in the JobWizard.

Complete Process of System Calibration

The described method of calibration intended for using the system with needles and/or printing heads from
other vendors when exact dimensions of needles and printing head are unknown. In this method of calibration
dimensions of the printing head and needle considered as ZERO. It is not necessary to measure exact dimensions
of the other vendor pins and head to perform calibration. In this case the ZERO POINT of the system is at the
tip of the printing pin. Process of calibration deals with consecutive touching of the system reference points
by the tip of the needle and registering system coordinates with the "ConfigureSystem" Utility

Before starting the calibration process it is necessary to create new type of printing head and printing pin
with zero dimensions. This type of pin and head will be used with all printing jobs the other vendor printing
head and pins will be used with. Parameters of the printing head and pin other than geometrical dimensions
(number of holes, pickup speed etc.) can be real, not equal to zero.

In the examples we assume that the printing head and printing pin from TeleChem are used in the system. Name
to the TeleChem head will be "ZERO_TC_head" and name for the TeleChem printing pins will be "ZERO_TC_pin".

Create ZERO printing head.

- Run ConfigureSystem program.
- In the "LabNext Equipment Configurator" window press "Edit" button next to the "Print Head Config" line.
- In the "LabNext Print Head Configuration Editor" window press "New" button next to the "Print Head Config name"
string.
- In the "New Print Head Config" window type a new name for the head configuration: “ZERO_for_calibration”.
Press the "OK" button.
- Press "Edit" button next to the "printHead" string.
- In the "Edit Print Head" window enter following values for the head parameters:
-- "description" = any description
-- "material" = metal
-- "thickness" = 0
-- "headOriginX" = 0
-- "headOriginY" = 0
-- "headOriginZ" = 0
-- "pinHolesX" = 4
-- "pinHolesY" = 4
-- "pinHoleStepX" = 4.5
-- "pinHoleStepY" = 4.5

- Press the "Save As" button. In the "Choose an object (Type PrintHead)" window type “ZERO_TC_head” in the
line at the bottom of the window. Press "Choose" button in the right side of the window.
- Close the "Edit Print Head" window.
- "LabNext Print Head Configuration Editor" window press the large button between the "printHead" string and
the "Edit" button. From the drop-down list select "ZERO_TC_head"

Create ZERO printing pin.

- In the "LabNext PrintHead configuration editor" window press "Edit" button next to the line "printPin".
- In the "Edit PrintPin" window press "New" button next to the line "PrintPin name".
- In the "New PrintPin" window enter “ZERO_TC_pin” and press "OK" button.
- In the "Edit PrintPin" window enter following values for the print pin parameters:
-- "description" = any string
-- "length" = 0
-- "shape" = round
-- "diameter" = 0.21
-- "safeDiameter" = 0.4
-- "pickupSpeed" = 1
-- "msPickupSubmergeTime" = 200
-- "glassDepositionTime" = 0.02
-- "nitroDepositionTime" = 0.01
-- "nylon DepositionTime" = 0.01

- Press "Save" button at the bottom of the "Edit PrintPin" window and close this window.
- "LabNext Print Head Configuration Editor" window press the large button between the "printPin" string and
"Edit" button. From the drop-down list select "ZERO_TC_pin"

- In the "LabNext Print Head Configuration Editor" window enter following values for the print head
configuration parameters:

-- "pinNumberX" = 1
-- "firstHoleX" = 0
-- "stepX" = 1
-- "pinNumberY" = 1
-- "firstHoleY" = 0
-- "stepY" = 1

- In the "LabNext Print Head Configuration Editor" window press the button between the "PrintHeadConfig name"
line and the "New" button. From the drop down list select "ZERO_for_calibration" entry.
- In the "LabNext Print Head Configuration Editor" window press button between the "printHead" line and "Edit"
button. From the drop-down list select "ZERO_TC_head" entry.
- In the "LabNext Print Head Configuration Editor" window press button between the "printPin" line and "Edit"
button. From the drop-down list select "ZERO_TC_pin" entry.

- Press "Save" button at the bottom of the "LabNext Print Head Configuration Editor" window.
- Close the "LabNext Print Head Configuration Editor" window.

Process of calibration.

Calibration is registering coordinates of reference points of the objects on the working board and height of
movement of the pin when the printing head passes from one object to another. Coordinates can be measured and
registered in the system memory by touching the reference point with the printing pin installed in the
printing head and pressing "Register" buttons next to the entry fields in the ConfigureSystem program.
To move robot from one point to another use manual controls provided by the ConfigureSystem program.

XYZ coordinates of the following objects must be measured and entered to the system.
- Work Board origin (left upper corner of the work board)
NOTE: Arrayers manufactured past 2007 do not have an integrated work board. Set Work Board origin
X = 0, Y = 0, Z = 0
- Slide Nest Origin (left upper corner of the left nearest slide)
- Plate Nest Origin (left far corner of the plate)
- Left nearest hole of the dryer
- Left nearest hole of the washer

- Safe Height (the height of transition over the working board without risk of hitting an object)
- Over Slide Nest Height (height of transition from slide to slide while printing)

Before you start calibration.

- Insert the pin that you will be using (TeleChem pin in this example) for printing in the printing head in
the position that shown at the picture.

x o o o
o o o o
o o o o
o o o o

- Install a glass slide into left nearest slide nest.
- Install a plate into the plate nest
- Power on the system.

Calibration of the robot

- In the "LabNext Equipment Configurator" window press "Edit" button next to the string "spotter".
- In the "LabNext Personal Microarrayer Calibrator" window press "New" button next to the "Spotter name"
string in the right window panel "Spotter parameters".
- In the "New Spotter" window enter "TC_pins_spotter" and press "OK".
- In the "Spotter parameters" panel press large button between the "Spotter name" string and the "New" button.
From the drop-down list select "TC_pin_spotter" entry.
- In the left panel "Robot controls" press "H" button. Wait till robot completes homing process.
- Press "Setup Pin Offset" button at the bottom of the right panel "Spotter parameters".
- In the "Measuring Pin position" window enter following values:
-- "X offset" = 0
-- "Y offset" = 0
-- "Z offset" = 0
and press "OK".

Safe Height
- Use "" "" "" arrow buttons in the "Robot controls" panel to move the system. Move the pin 3-5 mm over the
washing/drying station.
- Press "Register" button next to "safeHeight" field in the "Spotter parameters" panel of the "LabNext Personal
Microarrayer Calibrator" window. ( If there is an object higher than the washer/dryer station register
"safeHeight" 3-5 mm over the highest object on the work board. )

Work BoardOrigin

For arrayers manufactured past 2007 manually enter:
-- "workBoardOriginX" = 0
-- "workBoardOriginY" = 0
-- "workBoardOriginZ" = 0

For arrayers manufactured before 2007:
- Using manual controls move the head of the robot so that the tip of the pin touch the left-far-upper corner
of the work board. Press "Register" buttons next to the strings:

-- "workBoardOriginX"
-- "workBoardOriginY"
-- "workBoardOriginZ"

- Press the large button between the "xyzMotionSystemParameters" string and the "Edit" button in the "LabNext
Personal Microarrayer Calibrator" window. From the drop-down list select "Xact_3_0_params".
(ATTANTION: do NOT edit xyzMotionSystem parameters. If you pressed "Edit" button just close the
"XYZMotionSystemParameters" window without making any changes).

- Press "Save" button at the bottom of the " Spotter parameters" panel.

Work Board

Configure work board parameters.
After the workBoardOriginX Y Z has registered the system measures coordinates of the elements on the board
RELATIVE to the work board origin.

- Press "Edit" button next to the "workBoard" string at the bottom of the "Spotter parameters" panel.
- In the "WorkBoard editor" window press "New" button next to the "Work Board name" string.
- In the "New Work Board" window enter “TC_pin_work_board” and press "OK".
- In the "WorkBoard editor" window press "Save" button. Keep the "WorkBoard editor" window open.
- Using manual controls move the head so that the pins touch the far-left corner of the close-left glass slide.
Press "Register" button next to the following strings in the "WorkBoard editor" window:

Slide Nest
-- "slideNestOrigX"
-- "slideNestOrigY"
- Move the head to the nearest empty slide nest and touch the surface of the work board with the tip of the
needle. Press "Register" button next to the string:
-- "slideNestHeight"

Plate Nest

- Move the head to the plate nest with the plate installed in it. Touch with the tip of the needle far-left
corner of the plate. (NOT the well of the plate but CORNER) Press "Register" buttons next to the strings:

-- plateNestOrigX
-- plateNestOrigY

- Remove the plate from the nest.
- Move the head so that needle touch the surface of one of the four rubber disks in the corners of the plate
nest. Press "Register" button next to the string "plateNestHeight".

Dryer
- Move the head over the washer/dryer station. Position the pin over the close-left hole of the dryer and
slowly move it in the hole until the conical part of the pint is entirely in the hole. Adjust X and Y position
of the pin using slow moving controls " or " to hit the center of the hole with as accurate as possible.
(BE ACCURATE DO NOT MOVE THE HEAD SIDE-BY SIDE using the fest speed controls "" or "" when the needle is
inside the hole of the washer or dryer. USE ONLY low speed controls " or " ). When the pin positioned precisely
in the hole of dryer press "Register" buttons next to the following entry fields:

-- "dryerX"
-- "dryerY"
-- "dryerHeight"

Washer
- Position the pin over the close-left hole of the washer and slowly move it inside the washer chamber.
Adjust X Y position of the pin if necessary. When the pin is positioned in the center of the hole register
X and Y position by pressing "Register" buttons next to the entry fields:

-- "washerX0"
-- "washerY0"
-- "washerX1"
-- "washerY1"
Please note that "washerX0" = "washerX1" and "washerY0" = "washerY1" ALWAYS in this model of the robot. These
values may differ in the other models.

- Lift the pint over the hole of the washer and move over the area between the holes. Move the pin down until
it touches the cover of the washer/dryer station. Press "Register" button nest to the entry field:
-- "washerHeight"

- Manually enter to the "washerHeight" field value that is 10mm bigger than the value registered in the
previous step. This value indicates the water level in the washer chamber that is 10mm lower than the cover.
(EXAMPLE: if "washerHeight"= - 15.0 after touching the washer cover enter manually new value
"washerHeight" = - 5.0 )

Over Slide Nest Transition Height
- Move pin tip over any spring that holds glass slide in the slide holder. Move it down and stop about
1mm over the spring.

- In the "WorkBoard editor" window press "Register" button next to the "overSlideNestHeight" string.

- Press "Save" button in the "WorkBoard editor" window and close this window.

- Press the large button between the "workBoard" string and the "Edit" button. From the drop-down list select
"TC_pin_work_board"

- Press "Save" button in the "LabNext Personal Microarrayer Calibrator" window and close this window.

- Press "Save" button in the "LabNext Equipment Configurator" " window and close this window.

THIS IS THE END OF THE CALIBRATION.

REMOVE PINS FROM THE HEAD (if some parameter entered incorrectly the robot wont break the pin) and run "spotter"
program. If robot moves correctly insert one pin and check how accurately it goes into washer/dryer holes and
the microplate wells.

Using of the previously created print jobs with the new robot settings.

All printing jobs created for previous microarrayer head and printing pin settings can be used without
significant modifications. In order to use them with the new settings it is necessary to tell the system that
new pin and head parameters must be used with a previously created print job.

- Run "JobEditor" program.
- In the "LabNext Print Job Editor" window press button next to the "PrintJob name" string. From the drop-down
list select the print job you suppose to run.
- Press the button next to the "spotter" string. From the drop-down list select "TC_pin_spotter".
- Press "Edit" button next to the "printHeadConfig" string.
- In the "LabNextPrintHead configuration editor" click on the button next to the "printHead" string. From the
drop-down list select "ZERO_TC_head".
In the "LabNextPrintHead configuration editor" click on the button next to the "printPin" string. From the
drop-down list select "ZERO_TC_pin".
- Press "SaveAs" button at the bottom part of the in the "LabNextPrintHead configuration editor" window.
- In the "Choose an object (type PrintHeadConfig)" window type “TC_16_pins” (or whatever number of pins that
have been used previously with this print job) and press "Choose" button in the right panel of the window.
- In the "LabNextPrintHead configuration editor" window press "Save" button and close this window.

- In the "LabNext Print Job Editor" window press the button next to the "printHeadConfig" string. From the
drop-down list select "TC_16_pins".
- Press "Save" button in the "LabNext Print Job Editor" window and close this window.

THE PRINT JOB IS READY TO USE WITH THE NEW SETTINGS. This job can be started in a regular way in the
"Jobcontrol" utility string in the command prompt.