SDI Synbiosis ProtoCol 3 User manual

Measure
Select Measure tab.
Test Measure Plate.
Assign a plate ID.
Accept batch.
Click
Click
Click
Review zone
measurements If all zones are detected click
Finish, if not repeat step 8
and ensure all of the
zones are central.
11
Click
Identify zones
10 From Image click on an area of
the disc or well to pick colour,
repeat for zone and the
background. Be sure to take
representative samples
from across the plate.
Click Next.
Sample
Sample
Sample
ProtoCOL 3 is now ready to make the
first measurement
Synbiosis Europe and International Headquarters:
Beacon House Nuffield Road Cambridge CB4 1TF UK
Tel: [phone] Fax: [phone]
email: [e-mail]
Synbiosis USA Headquarters:
5123 Pegasus Court Suite Q Frederick MD 21704 USA
Tel: [phone]
email: [e-mail]
Website: www.synbiosis.com
All trademarks acknowledged A0029.06.19
26
SYNBIOSIS
PROTOCOL 3
QUICK GUIDE
12

Thank you for ordering your
Synbiosis ProtoCOL 3 automated
colony counter and zone sizing system.
If you ordered your device with a
touchscreen PC, please follow from
page 2 but ignore pages 5-13
(SOFTWARE INSTALLATION) as this
has already been completed for you.
Alternatively if you ordered your device
without a touchscreen PC, please follow
from page 5 onwards.
All guides and validation procedures
ordered will be located on the
computer’s desktop if you ordered
a PC, or on the installation USB,
if you didn’t.
Should you require any additional
assistance installing your device, please
contact [e-mail].
GETTING STARTEDCONTENTS
1
GETTING STARTED
CONNECTING YOUR TOUCH SCREEN PC
SOFTWARE INSTALLATION
HOW TO ADD A USER
COUNT VALIDATION PROCEDURE
1
2
5
14
18
ZONE VALIDATION PROCEDURE
TOTAL PLATE COUNT BATCH SET-UP
INHIBITION ZONE BATCH SET-UP
20
22
24

23
CONNECTING YOUR
TOUCH SCREEN PC
Attach bracket and
PC to ProtoCOL 3
body
Unpack ProtoCOL 3
Unpack the instrument and the
PC and place on a secure level
surface.
Attach monitor leads
Attach leads to PC
and monitor
Attach the leads to the PC and
to the monitor before securing
the monitor onto the bracket
(step 5). They are labelled to
help you.
Attach monitor to
PC/bracket
Slide the bracket (attached
to the monitor) over the top,
lining the two pins with holes in
monitor bracket - taking care
to feed the cables under the
monitor so as not to impede
the movement of the monitor.
Secure the monitor onto the
bracket using the 4 screws.
5
4
3
2
1
Attach the black bracket with
PC to the instrument via the
silver mounting plate as shown.
The four screws are secured
using a Phillips screwdriver
(not supplied).
Leave the three leads free
and sitting between the
bracket as shown.
Attach the 2 monitor leads to
the monitor before attaching
the monitor to the PC/bracket.
Ensure that the ferrite is
further from the monitor so
that it does not impede
monitor positioning.

5
4
Attach power cords to
the mains power blocks
There are 2 power leads found
at the back of the ProtoCOL 3
system. Attach the mains cables
provided to the power blocks
and plug into a socket.
THE DEFAULT LOGIN DETAILS FOR THE
PROTOCOL 3 PLUS ARE
Username:
P3Admin
Password:
The unit’s serial number in capitals
(located on the rear of the device)
SOFTWARE
INSTALLATION
Start PC
Log onto PC as an
Administrator and shut all
running software down.
Insert the Synbiosis USB flash drive
Browse to the flash drive in
Windows named ‘Software’.
Install Microsoft.net Framework
Run SetupFramework.exe. Follow the on-screen instructions,
performing a system restart if prompted. If you are prompted that
this program is already installed then proceed to the next step.
Install SQL Server Database
ProtoCOL 3 software requires Microsoft’s SQL Server.
If you already have a SQL server at a remote location press OK and
go to step 5, otherwise press Cancel and follow step 4.
Run SetupP3SqlServer.exe following on-screen instructions.
Install the ProtoCOL software
Run Setup.exe following on-screen instructions.
5
4
3
2
1
6

Press Next.
Select the device you
are using from the list
and press Next.
Select any additional
hardware you have
purchased from the
list then click Next.
6
Connect the
ProtoCOL 3
Connect the power cord to the
ProtoCOL 3 and plug the unit in.
Connect the camera USB cable
from the ProtoCOL 3 unit to a
spare USB port in the PC.
Switch on the ProtoCOL 3 using
the switch on the side of the
unit.
7
Press Next or select
an alternative folder.
Press Install.
Press Next.
Press Next or select
an alternative install
location.
9
8
7
6
13
12
11
10

8
Press Finish.
Press Next.
Press Install.
Press Install.
9
Press Next.
Press Finish.
The Database Updater
application will appear.
If this box disappears
after a few seconds
then skip to step 25.
If the box remains
on display then this
means the database
has not been created.
If this is the case then
press the blue button
with three dots and go
to step 22.
Press Finish.
21
20
19
18
17
16
15
14

10
Press the Update button.
If any database updates
are required they will be
applied and the dialog
will close.
The data paths window
will appear. Enter a name
for the database e.g.
(ProtoCOL DB).
Press the New Database
button (on the right hand
side of the Database
Name). You will see a
message saying
“Database Successfully
Created”, press OK, then
press OK again on the
Data Paths window.
23
22
Please Note:
After the installation of the camera and serial drivers the installer will check to
see if the user is running Windows 10. If you are installing ProtoCOL 3 on
a Windows 10 computer the installation wizard will not appear. Instead you
will be asked to confirm you are using a USB dongle to license the software.
If Windows 10 is being run then a prompt will appear with the dialog below.
If OK is selected, the dongle drivers will be updated to the correct version and
the install wizard will not run. The user will receive the following message:
“Completed USB dongle software installation. Please connect your USB
dongle licence following completion of the ProtoCOL 3 software installation”.
If Cancel is selected the normal install wizard will appear later so the media
key method of installing a licence can be used. The install licence is available
after installation via : Windows Start->Synbiosis->Support->Install Wizard
If the machine did not activate automatically
the licensing wizard will appear. Select the
appropriate method for licensing and press
Next. If using a hardware key (a USB
dongle) do not connect the key until
instructed to by the wizard. The pages that
follow will vary depending on the selection.
24
Enter the media key
provided in your
installation kit, also
located on the USB.
11
Software Key
Activation Method
Copy and paste the
information highlighted
in blue and email to
installations@synbiosis.
com.
An email will be sent
back with a security
code to use in the next
step. (Please note that
the email does not need
to be sent from the
device. The sender will
receive the code).
Enter the security code
received from
installations@synbiosis.
com and click Next.
Your activation is now
complete. Press Finish.

Add Users to user groups
HOW TO ADD A USER (page 14). This is an important step and the
device will not function correctly unless the users have
been set up.
27
12
25
Select the USB key.
Click Next.
Hardware Key
Activation Method
Remove all connected
USB dongles from the
PC.
Click Next.
Insert hardware key.
Click Next.
The installation is now
complete. Press Finish.
Press Finish.
The final page will vary
depending on the
licensing type.
13
Run the calibration
installer Browse to the
Synbiosis USB flash
drive in Windows
and open the
“Calibration” folder.
Run the
“SetupCalibration”
program and then
follow the on screen
instructions.
26
Run ProtoCOL 3
software
28
Log on to the software and ensure the lights cycle Red, Blue and
Green. Click on the image tab and select live image to ensure the
camera produces a live image.

14 15
HOW TO
ADD A USER
When ProtoCOL 3 is installed, three default
user groups are created:
ProtoCOL Admins
ProtoCOL Advanced Users
ProtoCOL Users
Every person using this device needs
to be a member of one of these groups
1Log onto system as Administrator
Access Computer Management
2
Access the Control panel.
Select System and Security.
Click on Administrative Tools.
Double click on Computer Management.
3Accessing the User Groups
Locate and double-click the ProtoCOL
Admins group.
Non Admin accounts need to be added to
the advanced or user level groups instead.
Select Groups.
Expand Local Users and Groups and click
on Group folder.

Add a Group of Users
5
To add a group
of users to a
ProtoCOL group
click Advanced
on the page
entitled
“Select Users,
Computers or
Groups”.
Then click Find
Now.
16 17
Add a Single User
To add a single
user, enter
their Windows
username in the
box labelled
“Enter the object
names to select”
and click Check
Names. Click OK
to return to the
ProtoCOL Admin
Properties
Dialog and the
user will have
been added to
the ProtoCOL
Admins group.
Click Add.
46Add a Group of Users (Cont)
Select the group
you want
to add and
click OK.
Click OK.
Click OK to close
the dialog.

18 19
COUNT VALIDATION
PROCEDURE
The purpose of this validation is to
confirm that the ProtoCOL 3 system
correctly uses contrast and background to
accurately count a set number of
entities in a known area.
Requirements:
ProtoCOL 3 / ProtoCOL 3 Plus System
Pour Plate Validation Plate(s)
ProtoCOL 3 User Manual
Familiarity with the ProtoCOL 3 software
Figure 1: Example of Pour Plate Validation Plate
Pour Plate Validation Procedure
1. Insert the pour plate validation plate into the ProtoCOL 3 and
close the doors to minimise ambient light.
2. Log on to the system, load the ProtoCOL 3 software and log on
to the software.
3. Next create your Validation Test batch by clicking “New Batch”.
4. Select “Pour Plate” from the module options.
5. Name the batch “Validation Test”.
6. Check the camera exposure by clicking on the “Image” tab and
adjusting the exposure as necessary and capturing the image, it
should be between 200-300 ms.
7. Adjust the graticule (circle) so it is around the colonies.
8. Click on the “Classification” tab and perform the “Colour
Classification” and choose one colour and click “Next”.
9. Set the “Small Particle Slider” to OFF and select the “Split”
option, click “Next”.
10. Click “Finish”.
11. Click on the “Measure” tab, enter a plate ID of ‘1’.
12. Perform a test measurement by clicking “Test Measure Plate”.
Ensure the count displayed matches that on the validation plate
(e.g. 100).
13. ‘Accept’ the batch.
14. Within the new batch, select the “Measure Plate” button and
review the result. The count should match what is stated on
the validation plate.

20 21
ZONE VALIDATION
PROCEDURE
The purpose of this validation is to
confirm that the ProtoCOL 3 system
correctly uses contrast and background
to accurately measure
known diameters.
Requirements:
ProtoCOL 3 system with zone reading
software
Zone Validation Plate
ProtoCOL 3 User Manual
Familiarity with the ProtoCOL 3 software
Figure 1: Example of Zone Validation Plate
Zone Validation Procedure
1. Insert the zone measurement validation plate into the
ProtoCOL 3.
2. Log on to the system, and then log onto the software.
3. Click New Batch.
4. Select “Inhibition Zone” from the module options.
5. Name the batch “Validation Test”.
6. Check the camera exposure by clicking on the “Image” tab and
adjusting the exposure as necessary between 200-250ms.
When image is acceptable click “Capture Image”.
7. Click the “Zone Classification” button, choose the “Ring”
configuration and leave the number set to 6. Adjust the size of
the zones as needed (if necessary, move individual zones by
checking the box entitled “Move Individual Zones”) to ensure
the black zones are directly in the centre of the
6 measurement frames and click “Next”.
8. Select “No Discs/Wells”, click “Next”.
9. Highlight “Zone Colour” and click on one of the black zones to
identify its colour. Highlight “Background Colour” and click on
the background to identify its colour, Click “Next”.
10. Review measurements. If any are offset repeat Classification
and ensure the black zones are directly in the centre of the
6 measurement frames.
11. Press “Finish”.
12. Complete the zone classification by selecting the
“Measure” tab and perform a test measurement by clicking
“Test Measure Plate”.
13. The measurements should be within +/- 0.5mm of those stated
on the validation plate.
14. On the “Measure” tab, assign a name/number to the plate ID.
15. Accept the Batch.

TOTAL PLATE COUNT
BATCH SET-UP
Start ProtoCOL 3 software
Log on to ProtoCOL 3.
1
2Position plate Insert the plate holder, ensuring
the plate holder used gives the
best contrast between the
colony and background.
Place plate onto plate holder.
3Capture image
Click
Slide
Click
Create batch
4
5Plate configuration Select Plate Configuration to set
plate size, sample volume and
threshold. Defaults are Circular
plate 90mm, Sample volume
1ml. Change if necessary.
6Choose an application
Click New Batch.
Click
Select
Select Pour Plate.
Select 23
7Name the batch
Name the batch.
8
Position the counting
frame over the colonies
to be counted.
Click Total Plate Count.
Select colony type from
the drop-down, either
Light or Dark Colonies.
Total plate count
Click
Click
Select
9Move slider to the left to
adjust the detection
sensitivity.
Move slider to the left to
accept small particles or
to the right to exclude
small particles.
If any colonies are
touching select the
Split function.
Classification settings
Slide
Check
10
Enter a plate ID found
on Measure tab.
Auto-increment
default is “on”, to change
this click on the
Configuration tab.
Enter a plate ID
Enter
Click
11 Accept batch
ProtoCOL 3 is now
ready to make the first
measurement
Enter
Click
22
Enter
Select the image tab and check
the live box.
Adjust the exposure by
increasing/ decreasing the
sliding scale.
Capture image.

INHIBITION ZONE
BATCH SET-UP
Start ProtoCOL 3 software
Log on to ProtoCOL 3.
1
2Position plate Insert the plate holder, ensuring
the plate holder used gives the
best contrast between the
zone and background.
Place plate onto plate holder.
3
Select the image tab and check
the live box.
Adjust the exposure by
increasing/ decreasing the
sliding scale.
Capture image.
Capture image
Click
Slide
Click
Create batch
4
5Plate configuration
Click New Batch.
Click
Select
24 25
6Choose an application
Select Inhibition Zone.
Select
7Name the batch
Name the batch.
Enter
Enter
Select Plate Configuration to set
plate size, sample volume and
threshold.
Zone classification
Select
Click
Click
Select Zone Classification tab.
Select type of zone frame and
the number of zones required.
Position the grid directly over
the zones. To move individual
measuring circles check the box
and setting circle to the
maximum zone size.
Zones can also be named on
this page by clicking Rename
Zones.
9Indicate whether discs or wells
are present.
If a well or disc is present enter
the size of disc/well by entering
the size directly into the box or
by clicking on the text box and
drag the circle to just outside
the edge of the well or disc.
Click Next.
Discs/wells present
Enter
or
8