UVP ColonyDoc-It User manual

ColonyDoc-It™Imaging Station
Instruction Manual
UVP, LLC Ultra-Violet Products Ltd.
2066 W 11th Street, Upland, CA 91786 Unit 1, Trinity Hall Farm Estate
Tel: [phone] Nuffield Road, Cambridge CB4 1TG UK
Fax: [phone] Tel: [phone] / Fax: [phone]
Email: [email protected] Email: [email protected]
Web site: uvp.com
81-0294-01 Rev. E

ColonyDoc-It Imaging Station 2

ColonyDoc-It Imaging Station 3
END USER LICENSE AGREEMENT
PLEASE READ THE FOLLOWING AGREEMENT CAREFULLY
This Agreement is between UVP, LLC of 2066 West 11th Street, Upland, California 91786 (hereinafter “Licensor”) and the
end user of UVP software (hereinafter “Licensee”).
Licensor has developed and offers to Licensee on a non-exclusive basis pursuant to the terms and conditions set forth
hereinafter, the following software, including related copyrighted instructional materials, (collectively referred to hereafter as
“The Software”):
DOC-IT COLONY SOFTWARE
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most common medium for acquiring the Software from Licensor is by CD-ROM, the Software may, in some instances, be
acquired by download; from a Licensor thumb drive acquired from Licensor; from a CD ROM acquired from Licensor from a
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incorporated in or generated by the software, and data accompanying this License and related documentation are licensed
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LIMITED WARRANTY AND DISCLAIMER
Licensor warrants the software and related documentation to be free from defects in materials and workmanship, under
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reliability, or otherwise. The limitations of liabilities described in this section also apply to the third party suppliers of
materials used in the software. No oral or written information or advice by licensor or by representatives of licensor shall

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create warranties, and/or conditions, or in any way increase the scope of this limited warranty. Licensee assumes the entire
cost of all necessary servicing, repair or correction after the ninety (90) days. Some jurisdictions do not allow the exclusion
of implied warranties, so the above exclusion may not apply to you.
LIMITATION OF LIABILITY
Under no circumstances, including negligence, shall licensor be liable for any special or consequential damages that result
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licensor has been advised of the possibility of such damages. Some jurisdictions do not allow the limitation or exclusion or
liability or consequential damages, so the above limitations or exclusion may not apply to you. In no event shall licensor‟s
total liability to you for all damages, losses, and causes of action (whether in contract, tort (including negligence) or
otherwise) exceed the amount paid by you for the software.
INTENDED USE
If the equipment is used in a manner not specified by the manufacturer, the protection provided by the equipment may be
impaired.
GOVERNING LAW AND SEVERABILITY
This License shall be governed by and construed in accordance with the laws of the State of California, without giving effect
to any principles of conflicts of law. Any actions, suits or proceedings instituted in connection with this License, the Software
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you hereby consent to the venue and jurisdiction of the aforesaid courts. If any provision of this license shall be unlawful,
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the validity and enforceability of any remaining provision. This is the entire agreement between the parties relating to the
subject matter herein and shall not be modified except in writing, signed by both parties.

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Table of Contents
Introduction ............................................................................................................................................................................... 7
Components ............................................................................................................................................................................. 7
System Requirements............................................................................................................................................................... 8
System Specifications ............................................................................................................................................................... 8
Installing the ColonyDoc-It ........................................................................................................................................................ 9
Installing the Hardware ............................................................................................................................................... 9
Installing the Software .............................................................................................................................................. 11
Registering the Software .......................................................................................................................................... 11
Counting Colonies .................................................................................................................................................................. 13
Quick Capture ........................................................................................................................................................... 13
Automatic Counting .................................................................................................................................................. 15
Manual Counting ...................................................................................................................................................... 16
Creating Templates .................................................................................................................................................. 20
User Defined Template Counting ............................................................................................................................. 21
Fluorescent Colony Counting ................................................................................................................................... 22
Zone Analysis ........................................................................................................................................................... 24
Renumbering Colony/Zone Values ........................................................................................................................... 28
Spiral Plate Counting ................................................................................................................................................ 29
Editing Colonies ...................................................................................................................................................................... 31
Add Colonies ............................................................................................................................................................ 31
Delete Colonies ........................................................................................................................................................ 32
Manual Split Colonies ............................................................................................................................................... 33
Auto Split Colonies ................................................................................................................................................... 34
Merging Colonies ...................................................................................................................................................... 35
Using the Software ................................................................................................................................................................. 36
Changing Filter Settings ........................................................................................................................................... 36
Preferences .............................................................................................................................................................. 37
Toolbars ................................................................................................................................................................... 39
Reporting Functions ................................................................................................................................................................ 40
Classes ..................................................................................................................................................................... 40
Colonies ................................................................................................................................................................... 41
Statistics ................................................................................................................................................................... 41
Distribution................................................................................................................................................................ 42
Exporting to Excel ..................................................................................................................................................... 42
Supporting 21 CFR Part-11 Compliance................................................................................................................................. 44
Purpose .................................................................................................................................................................... 44
Features ................................................................................................................................................................... 44

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Usage ....................................................................................................................................................................... 44
Servicing the ColonyDoc-It ..................................................................................................................................................... 45
Cleaning and Care .................................................................................................................................................... 45
Replacing Switches .................................................................................................................................................. 46
Replacing Fuses ....................................................................................................................................................... 46
Ordering Replacement Parts and Accessories ......................................................................................................... 46
Troubleshooting ........................................................................................................................................................ 46
Return Service Procedure ........................................................................................................................................ 47
Technical Support ..................................................................................................................................................... 48
Warranty ................................................................................................................................................................................. 48

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Introduction
This manual covers the installation and user instructions for the ColonyDoc-It Imaging Station.
The innovative, compact design enables users to process automated, fast and accurate colony counting. The high
resolution digital color camera allows users to capture white light and fluorescent marked colonies and a wide array
of samples. The sophisticated yet intuitive system offers researchers easy detection and analysis of media.
The software loads on the user‟s computer for camera control, image capture and colony counting. The software
provides automatic and manual counting capabilities plus user defined templates for speeding up research
experiments. Users can define specific counting parameters including color differentiation and filter identification by
group or size. Once the colonies are counted, the results display on the screen. Images and data can be saved in
multiple formats and the data can be exported to Excel. The software supports 21 CFR Part 11 compliance.
Components
 Colony counter
 Black plate
 USB cord
 Power cord
 Software CD

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System Requirements
 Operating System: Windows XP Professional with Service Pack-2 (32 bit only), Vista (32 bit only),
Windows 7 (32 bit only)
 Internet Explorer 6.0 or higher (To determine the version of Internet Explorer, open Internet Explorer and
click on Help > About)
 Minimum resolution: 1024 x 768
 Intel Pentium Processor or equivalent, 1.6 GHz or higher
 1GB (2GB recommended) of RAM or greater
 200 MB of available hard disk space for the program, more for data
 To avail the functionality of 21 CFR Part 11, then the partition must be formatted with NTFS.
 CD-ROM drive
System Specifications
Electrical ratings:
Model Numbers:
97-0539-01, 97-0539-04
100-115V, 60Hz, 0.25 Amps
Model Numbers:
97-0539-02, 97-0539-05
230V, 50Hz, 0.13 Amps
Operational Ratings:
Unit intended to be used indoors
Altitude must not exceed 2000 m
Operating temperatures not to exceed 0°C to 40°C (32°F to 104°F)
Operating humidity not to exceed 85%

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Installing the ColonyDoc-It
Installing the Hardware
Set the ColonyDoc-It Imaging Station on a
level surface.
Plug in one end of the power cord to the back
of the ColonyDoc-It Imaging Station and the
other end into a power outlet. To maintain
safety at all times, ensure that the unit is not
hard to disconnect at the location chosen.
Turn on the ColonyDoc-It by switching the I/0
switch to I located at the back of the station.
Plug one end of the USB cord to the back of
the ColonyDoc-It and the other end into a USB
port in the computer.
Removing the Doors
The ColonyDoc-It doors can be removed by
hand-loosening the two thumbnuts on the
inside of each door.

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Installing the Filter
Note: Filters come as an optional accessory so this step is only necessary if an optical filter will be used with the
system.
The filter trays are located in the filter box attached to the ceiling of the unit. To access the trays:
Remove the four brass thumbnuts on the
filter box and pull the filter box from the
housing.
Remove the two thumbnuts that hold the filter
frame to the filter box.
 Place the filter over the opening.
 Replace the filter frame and thumbnuts.
 Reinstall the filter box into the unit.
NOTE: It is possible to install a filter when the
filter box is installed in the unit. However,
care must be taken to avoid touching the
shiny sides of the filter.

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Installing the Software
Insert the Doc-It Colony Counter CD into the CD drive in the computer.
The InstallShield Wizard window will
appear.
Follow the instructions for installation.
Once installation is complete, refer to the
Registering the Software in this manual to
activate the software.
Registering the Software
Opening the Software
Double click the software icon on the
desktop.
To activate the software, registration is
required. To immediately activate the
software through the internet, choose On
the fly activation. If the computer is not
connected to the internet, please follow the
instructions for Offline activation or call
UVP to register the software.
Click Next to continue.

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Complete all required information on the
form.
Fill out the Serial Number located on the
CD. The number should be four sets of six
numbers.
Click onto Get Activation No. and then
click onto Activate when the Activation
Number appears in the box.
Already have an activation ID is useful
when reloading the software after receiving
an initial activation code.
If the computer is not connected to the
internet, click Offline activation to register
the software. This allows the user to obtain
the activation code and enter it at another
time.
Click Next to continue.
Click the link provided and complete the
form to obtain instructions. Click Finish.

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Counting Colonies
Quick Capture
Place the Petri dish to be counted on the transillumination surface.
Select the appropriate lighting option for the sample. If unsure, turn the selector switch (located on the front of the
colony counter) to Base Lighting > Trans and remove the black plate (if present). The Trans lighting option will
apply to most applications.
If the colony counter is not already open, double click onto the Doc-It Colony Counter icon on the desktop.
Ensure that the Camera Control module is active. See the image of the screen below noted by the green circle.
The text must be black as shown. If the Camera Control is inactive (with grey text) proceed to the troubleshooting
section: Inactive Camera Window.
Select the Petri dish plate diameter from the Camera Control module. The choices are 6cm, 10cm, and 15cm.
Select the smallest colony size for this plate. The choices are <1mm and 1mm+. If <1mm is selected the
smallest colony size is below 1mm. The count will be faster if 1mm+ is chosen.
Choose the White Light option from Colony Lighting. The Dim to Bright slider will be disabled unless using the
Fluorescent Colony Lighting option. If counting fluorescent colonies go to the Fluorescent Colony Counting
section of the manual.

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Insert the Petri dish inside the colony counter.
Click the Preview button in the Camera Control module
and move the Petri dish until it is centered inside the red
circle. The outer red circle should fall just inside the Petri
dish outer edge. If it does not, make sure that the correct
Plate Diameter size was selected.
There are two focusing methods provided for imaging.
The first is Auto focus. Auto focusing allows the camera
to automatically find the appropriate focus for the sample.
Manual focus is provided should the camera need
intervention from the user to more clearly picture the
image.
Manual focus buttons allow users to adjust the focus in
small increments or large increments .
Brightness adjusts the brightness of the image.
Click the Capture button from the Camera Control
module to take a picture.
Click Start Colony Count in the Colony Count module at
the left of the screen to start the counting process.
Select Automated Count or Manual Count. Go to the
Automatic Count section in the manual to complete steps
for automated count. Go to the Manual Count section in
the manual to complete steps for the manual count.
NOTE: The User Defined Template Count is grayed out initially because there are no templates created.
Template counting allows users to create counting templates for frequently counted Petri dish plates. The manual
count process must be performed before template settings can be established.
TIP: The ColonyDoc-It doors can be easily removed if fluorescent colonies will not be counted. Go to the Removing
ColonyDoc-It Doors section in this manual for instructions.

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Lighting Tips:
There are four options for lighting the Petri dish. Epi Lighting options include White light and Blue light and
these sources light the Petri dish from the top. Base Lighting options include Trans and Darkfield and
these sources light the Petri dish from the bottom
Blue light is used to excite GFP stained colonies.
A majority of samples prepared using the spread method and a transparent substrate that are bacterial,
yeast, or mold are best viewed using Base Lighting > Trans.
If there is excessive handwriting on the bottom of the Petri dish, membrane paper, or stickers, then use Epi
Lighting > White or Base Lighting > Darkfield.
Use Base Lighting > Darkfield when counting a pour plate.
Using the black plate on top of the transillumination surface in combination with Epi Lighting sources
provides contrast that improves colony counting results.
Preparing Samples:
When preparing samples, write on the bottom edge away from the center of the Petri dish to increase
counting accuracy.
Automatic Counting
Before proceeding through the automatic counting steps, ensure that an image of the Petri dish has been captured
and is ready for analysis. See instructions on Quick Capture in this manual for more information on how to capture
an image.
Select Start Colony Count along the
left side of the screen. A new Colony
Count Type Selection window
appears. Select Automated Count
and OK.

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The automated count will be
displayed on the left hand side of the
screen.
Colonies can be filled in with red (as
depicted here) or outlined. Colonies
can also be numbered or annotated
using multiple colors. Go to the
Preferences section of this manual for
more details concerning changing the
appearance of the image.
If desired, colonies can be added,
deleted, split, or merged. Refer to the
respective sections of this manual for
instructions on using these tools.
Manual Counting
Before proceeding through the manual counting steps, ensure that an image of the Petri dish has been captured
and is ready for analysis. See instructions on Quick Capture in this manual for more information on how to capture
an image.
Select Start Colony Count along
the left side of the screen. A new
Colony Count Type Selection
window appears.
Select Manual Count and OK.
The Manual Count Colony Wizard
will open.

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Step 1: Select Classes
The window that appears after choosing
Manual Count is the Manual Count
Colony Wizard. It contains two tabs.
The first tab is Step 1 of 2: Select Classes,
the second tab is Step 2 of 2: Finish.
The first tab allows the user to define the
region of interest inside the Petri dish to be
analyzed. The region of interest is
identified by a green circle that should
include all the colonies of interest in the
Petri dish. The software automatically
defines the region of interest but by clicking
the Define Counting Region button the
user can increase or decrease the circle
size as needed.
If a smaller or larger region of interest is
desired, click onto the Define Counting
Region button and hold and drag the
pointer over one of the corners of the circle
to change the size. Or click inside the green
circle to move the entire region of interest.

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Sometimes applying Background
Correction to an image improves the
count.
To apply background correction click onto
the Background Correction button.
The image to the left depicts the resulting
flattened image.
The Select Classes tab allows users to
select the number of classes and colonies
in the Petri dish sample.
To count the desired colonies, ensure that
the Add Points button is highlighted in
yellow and click on a colony to be
counted in the original image of the Petri
dish. (A smaller duplicate image of the
original is present in the Step 1 of 2:
Select classes tab, but a colony cannot
be selected from this image.)
Classes are defined as different types of
bacteria, yeast, or mold present on the
sample. The software can detect various
types of classes in one dish. To add a
class, click onto the Add button in the
Classes section of the window.
Click on a colony

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Once the first colony is selected, the new
image in the Step 1 of 2: Select classes
window will show a black background
along with all of the colonies that contain
the same color as the point identified in
the Analysis Details window.
Adjust the Point Sensitivity slider to
increase or decrease sensitivity.
Increasing and decreasing sensitivity
almost always improves the final count.
Continue clicking on colonies in the
captured image to add points and adjust
the Point Sensitivity as necessary until
the black and white image shows all the
colonies of interest identified in white.
To remove points or classes from the
Analysis Details window, highlight the
point and select Remove Point or
highlight the class and select Remove.
Click the Count button to proceed to the
next tab.
NOTE: The Step 1 of 2: Select classes tab allows the settings created in this window to be saved in a user defined
template. If there are no templates created, the drop down menu will list Default as the only template option. Go to the
Templates section of this manual for instructions on creating templates.
Step 2: Finish
The software will automatically move to the
second tab Step 2 of 2: Finish after Count
is selected in Step 1 of 2: Select classes.
To filter the colonies, adjust the shape or
colony size in the Filter colonies section.
Change slider buttons for shape (from
circular to irregular) and size (1 pixel to 200
pixels) to capture additional colonies or
eliminate colonies.
This window is a second means to save
settings into templates. Go to the
Templates section of this manual for
instructions on creating templates.
Click Finish to exit the manual count mode
and to get the final count.

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Creating Templates
Templates allow the user to set colony counting parameters so that plates with similar properties are counted
quickly and consistently.
To set a template for any Petri dish, choose Start Colony Count (or Restart Colony Count if the Petri dish has
been counted before) in the Colony Count module, then select the Manual Count function. A template can be
saved during operation Step 1 of 2: Select classes or Step 2 of 2: Finish.
To save a template in Step 1 of 2: Select
classes, add the desired points and classes if not
already selected) and click the New button in the
Template section of the window.
If additional information is needed, refer to the
Manual Count instructions in this manual.
A New Template pop-up window will ask for a
new Template name.
Type in the new name and select OK.
The Template name window will close and direct
back to the Step 1 of 2: Select classes tab.
Click on the Count button to proceed to the Step
2 of 2: Finish tab.