UVP ColonyDoc-It Imaging Station 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: [e-mail] Email: [e-mail]

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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ColonyDoc-It Imaging Station 4

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If the equipment is used in a manner not specified by the manufacturer, the protection provided by the equipment may be
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subject matter herein and shall not be modified except in writing, signed by both parties.

ColonyDoc-It Imaging Station 5

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

ColonyDoc-It Imaging Station 7

 Colony counter

 Black plate

 USB cord

 Power cord

 Software CD

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

ColonyDoc-It Imaging Station 8

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%

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

ColonyDoc-It Imaging Station 9

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.

The ColonyDoc-It doors can be removed by
hand-loosening the two thumbnuts on the
inside of each door.

Installing the ColonyDoc-It

Installing the Hardware

Removing the Doors

ColonyDoc-It Imaging Station 10

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.

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:

ColonyDoc-It Imaging Station 11

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.

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.

Installing the Software

Insert the Doc-It Colony Counter CD into the CD drive in the computer.

Registering the Software

Opening the Software

ColonyDoc-It Imaging Station 12

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.

ColonyDoc-It Imaging Station 13

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.

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.

ColonyDoc-It Imaging Station 14

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.

ColonyDoc-It Imaging Station 15

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.

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.

Automatic Counting

ColonyDoc-It Imaging Station 16

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.

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.

Manual Counting

ColonyDoc-It Imaging Station 17

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.

Step 1: Select Classes

ColonyDoc-It Imaging Station 18

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

ColonyDoc-It Imaging Station 19

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.

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.

Step 2: Finish

ColonyDoc-It Imaging Station 20

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.

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.

ColonyDoc-It Imaging Station 21

If the shape and size sliders are changed to
capture additional colonies, click Create template
in the Templates section of the window to save
the new settings.

Select Finish to complete the count and save the
template.

NOTE: Templates may also be saved directly in
Step 2 of 2: Finish. Users may bypass the
template creation option in Step 1 of 2: Select
classes and go directly to Step 2 of 2: Finish to

create a template.

NOTE: If a template has been saved previously, the software will pull it in automatically to be used in
any Manual Counting process.

Select Start Colony Count, and then select User
Defined Template Counting, and use the
dropdown menu to select the desired template.

Click OK.

User Defined Template Counting

Before proceeding through the next steps, a template must have been saved during the manual count process. If

there are no templates, go to the Creating Templates section of the manual to create a template.

ColonyDoc-It Imaging Station 22

The new window will display the Total colonies
counted.
Ensure that the doors are attached to the
ColonyDoc-It or turn off the surrounding lights.

Turn the Epi Lighting switch on the ColonyDoc-It
to Blue.

Insert the Green Fluorescent Protein (GFP)
emission filter into either tray (refer to the

Installing the Filter section of this manual for

instructions) and ensure that the filter is positioned
below the camera. (If the GFP filter is in filter
position one, the filter slider should be moved all
the way to the right position.)

Insert the fluorescently stained sample into the
ColonyDoc-It.

Select the appropriate Plate Diameter, the

Smallest Colony information and choose the
Fluorescent lighting function of Colony Lighting

in the Doc-It Colony Counter software.

The slider bar may be adjusted from Dim to
Bright to provide optimum results.

Select Preview to position the plate inside the red
circle guides and then select Capture when the
image is positioned properly.

Fluorescent Colony Counting

ColonyDoc-It Imaging Station 23

Finally, choose to count the colonies
automatically, manually, or with a template.

Refer to the Automatic Count, Manual Count, or
Template Count instructions in this manual for

additional information.

ColonyDoc-It Imaging Station 24

Before proceeding through the zone analysis process, 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.

To obtain zone analysis information for a
plate, click on the checkbox for Zone
then select Start Colony Count.

Choose to count with the Manual or User
Defined method.

Click OK.

If using the software for the first time, no
templates are created and the User
Defined Template Count option
appears grey. To create a template, first
proceed through the Manual Count
functions to store settings.

First click
on Zone

Second click on

Start Colony Count

Zone Analysis

Zone analysis provides users with zone sizing information useful for applications such as inhibition zone analysis.

ColonyDoc-It Imaging Station 25

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 zones 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.

Step 1: Select classes

ColonyDoc-It Imaging Station 26

The Select Classes tab allows
users to select the number of
classes and zones in the Petri dish
sample.

To analyze the desired zones,
ensure that the Add Points button
is highlighted in yellow and click

on a zone 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 zone
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.

Once the first zone is selected, the
new image in the Step 1 of 2:
Select classes window will show
a black background along with all
of the zones that contain the same
color as the point identified in the
Analysis Details window.

Continue clicking on zones to add
points as necessary until the black
and white image shows all the
zones 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.

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.

Click the Count button to proceed
to the next step.

Click on a zone

ColonyDoc-It Imaging Station 27

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 add or subtract zones, change
the slider buttons for shape
(circular to irregular) and size (1
pixel to 200 pixels) until all the
zones of interest are highlighted.

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 view the results
table.

The software will redirect to the
initial screen and display the total
number of zones identified.

To view the analysis data for the
zones click onto Show Results
Window from the Main Tools
section of the Colony Count
module. A window appears that
provides information relating to the
classes, zones (listed as colonies),
statistics, and distribution of the
zones. In the report, users may
view the area and perimeter of the
zone.

To learn more about reporting

capabilities, go to the Reporting
Functions section of this manual.

Step 2: Finish

ColonyDoc-It Imaging Station 28

To enable easier statistical reporting of
each colony or zone, the values assigned
to each colony or zone may be
renumbered.

To renumber the values assigned to each
colony or zone click Recompute Colony

Labels under the Grid Analysis Tools.

NOTE: The plate must have already been

counted.

The Recompute Colony Labels function
will read the plate from left to right and
from top to bottom. So the colony (or
zone) labeled 1 will be seated at the left
and towards the top of the plate.

Before applying “Recompute Colony
Labels” function

After applying “Recompute Colony Labels”
function

Renumbering Colony/Zone Values

ColonyDoc-It Imaging Station 29

To perform a spiral plate count
click onto the Spiral checkbox
and then select Start Colony

Count.

Next, select from the Automated
Count, Manual Count or User
Defined Template Count.

NOTE: If using the software for

the first time, no templates are
created and the User Defined
Template Count option appears
grey. To create a template, first
proceed through the Manual
Count functions to store settings.

Additional instruction on

performing an Automated Count,

Manual Count, or Template
Count is listed in detail in this

manual.

After performing a count, a
Spiral Plate Analysis window
will appear along with a green
grid over the counted image.

To change the overlay grid size,
move the Overlay Size slider bar
to the left (to decrease the grid
size) or to the right (to increase
the grid size).

To calculate the SPLC/mL, type
in or use the up or down arrows
in the Total volume deposited
box provided. The calculated
amount will appear immediately
below the Calculate SPLC/mL
button.

First click
onto Spiral

Second click onto

Start Colony Count

Spiral Plate Counting

ColonyDoc-It Imaging Station 30

To view the resulting Data Table
analysis for the spiral plate
count, click onto the + sign
(expanded report shown here
after clicking the + sign). The
values listed will provide the
number of colonies found in each
quadrant and section of the
counted plate.

To save the spiral plate settings
in a template, click onto Save As
and provide a name for the
template.

To print or export the data into
Excel, click onto the Print or
Export to Excel button.

While in the Spiral Plate
Analysis window, the user may
choose to move the green
overlay grid by using the Align

Spiral Plate Overlay.

To move the grid, click onto
Align Spiral Plate Overlay, click
and drag the green grid until the
center of the grid is aligned with
the center of the captured image.

To clear the spiral plate analysis,
click onto the Clear Spiral Plate
Analysis. This action will
remove the data entered for this
plate and remove the spiral plate
grid.

Spiral plate analysis may be
performed on any counted plate.
To perform the spiral plate
analysis any previously counted
plate, select the Spiral Plate
Analysis option directly above
the Align Spiral Plate Overlay
option.

ColonyDoc-It Imaging Station 31

Users may add colonies by performing the initial count (Automated Count, Manual Count, or User Defined
Template Count), and adding colonies manually.

To add colonies, ensure that
the Add Colonies tab in the
Colony Count module is
highlighted in yellow.

If the colony is hard to see,
zoom in on the colony. In the
Zoom/Pan module, move the
slider button towards the +
sign on the right to zoom in.
A rectangular object will
appear in the Zoom/Pan
module. Move it over the
area of interest. The central
Petri dish image will appear
larger in the area identified by
the rectangular object.

Click on a colony to add.

The colony selected will now
have a circle (filled in or
outlined) around the point
selected.

The Total colonies count will
change to include the
colonies added.

Added Colony

Editing Colonies

Add Colonies

ColonyDoc-It Imaging Station 32

To use a larger circle to
highlight the colony, go to the
Analysis Display Settings.
A new window will open.
Browse to Main Settings >
Analysis > Colony Count.

In the Add Tool section of
the window, use the drop
down menu to select between
a Circle Radius of 5, 10, 15,
or 20.

Users may delete colonies after performing the initial count (Automated Count, Manual Count, or User Defined
Template Count), and deleting colonies manually.

To delete colonies from the
Total Colonies count, ensure
that the Delete Colonies tab is
highlighted in yellow.

If the colony is hard to see,
zoom in on the colony. In the
Zoom/Pan module, move the
slider button towards the + sign
on the right to zoom in. A
rectangular object will appear in
the Zoom/Pan module. Move it
over the area of interest. The
central Petri dish image will
appear larger in the area
identified by the rectangular
object.

Click on a colony to delete.

Delete Colonies

ColonyDoc-It Imaging Station 33

The colony circle (filled in or
outlined) will now disappear.
The Total colonies count will
change to remove the colonies
deleted.

Users may split colonies by performing the initial count (Automated Count, Manual Count, or User Defined
Template Count), and splitting colonies manually. Colonies should be split when two or more colonies are very
close together and are counted as one colony by the software.

To split colonies, ensure that
the Manual Split Colonies tab
is highlighted in yellow.

A new window will ask the user
to “Draw lines through the
colonies you want to split then
release.”

If the colony is hard to see,
zoom in on the colony. In the
Zoom/Pan module, move the
slider button towards the +
sign on the right to zoom in. A
rectangular object will appear
in the Zoom/Pan module.
Move it over the area of
interest. The central Petri dish
image will appear larger in the
area identified by the
rectangular object.

Deleted Colony

Manual Split Colonies

ColonyDoc-It Imaging Station 34

Draw lines through two or
more colonies that are close
together and treated as one.
Use the pointer and, while
holding the left mouse button
down, move from one edge of
the colony to the other.

The Total colonies count will
change to add new colonies
identified by the split.

Users may split colonies by performing the initial count (Automated Count, Manual Count, or User Defined
Template Count), and splitting colonies by clicking on the colony to split. Colonies should be split when two or
more colonies are very close together and are counted as one colony by the software.

To split colonies, ensure that the Auto Split Colonies tab is highlighted in yellow.

If the colony is hard to see, zoom in on the colony. In the Zoom/Pan module, move the slider button towards the +
sign on the right to zoom in. A rectangular object will appear in the Zoom/Pan module. Move it over the area of
interest. The central Petri dish image will appear larger in the area identified by the rectangular object.

Click onto the colony to split.

If the colonies are hard to see, zoom in on the colonies. Refer to the Zoom/Pan section of this manual.

The Total colonies count will change to add new colonies identified by the split.

Split Colonies

Auto Split Colonies

ColonyDoc-It Imaging Station 35

Users may merge colonies by performing the initial count (Automated Count, Manual Count, or User Defined
Template Count), and merging colonies manually. Colonies should be merged when one colony is treated as
two separate colonies by the software. Colonies will only be merged if they are less than 4 pixels apart.

To merge colonies, ensure
that the Merge Colonies tab
is highlighted in yellow.

A new window will ask the
user to “Select the desired
colonies and then press
Merge button to join them.”

If the colony is hard to see,
zoom in on the colony. In the
Zoom/Pan module, move the
slider button towards the +
sign on the right to zoom in.
A rectangular object will
appear in the Zoom/Pan
module. Move it over the
area of interest. The central
Petri dish image will appear
larger in the area identified by
the rectangular object.

Click onto the colonies to be
merged.

The Total colonies count will
now reflect changes due to
merging the colonies.

Merged Colony

Merging Colonies

ColonyDoc-It Imaging Station 36

To set new filter parameters, click onto
the Show Results Window > Filter >
Filter class and drag the pointer to the
filter class to change.

A new Filter Colonies window will
appear with the following parameters:

Area, Perimeter, Avg Diameter, and
Circularity.

The predefined ranges are defined.
Each parameter can be changed to
accommodate a wide variety of sample
types.

The new range can either be inclusive or exclusive. Click onto the Keep Range or Exclude range depending on
sample requirements.

Enter the values to keep or exclude. Click OK.

The software will recount the colonies based on the new filter values.

Using the Software

Changing Filter Settings

To reduce user initial set-up time, filters were created to count “true” colonies and remove inherent defects from the
sample plate that would (without the filters) be included in the total colony count. The filters may prevent a colony
from being counted based on some critical parameters.

ColonyDoc-It Imaging Station 37

To change the Label Type, from the
Analysis > Colony Count
preferences window, click the drop
down arrow and select from:

 None

 Class

 Number (general)

 Number (in class)

To change the Colony Marking, click
the drop down arrow to select from:

 None

 Outline

 Fill

To change the Label Color, click Auto
or click the drop down arrow and
select from the colors listed.

Preferences

Open the Preferences window from File > Preferences. This window allows users to set new defaults for the
display options, label color, annotation, camera template settings and miscellaneous functions such as annotation.

ColonyDoc-It Imaging Station 38

To change the Circle Radius, click the
drop down arrow and select from the
numbers to change circle pixel radius.

The Cameras > Canon Camera
preferences window allows users to
save modified template settings after
disconnecting. Choose from:

 Ask

 Always

 Never

To change the Text Annotation
Behavior, select from:

 Synchronize size with image

zoom which reduces/increases
the size of the annotations when
the size of image is
reduced/increased

 Don’t synchronize with image

zoom which maintains the size of
the annotations if the image is
reduced or increased

ColonyDoc-It Imaging Station 39

The Logging preferences window
allows the user to define the log file
path and the log level.

To change the Log File Path, click …
and locate a new directory.

To change the Log Level, click the
drop down arrow and select from the
list.

Toolbars

The toolbars allows users to select most commands with a single button click. The toolbars are customizable to
allow users the flexibility of including the commands used most and remove commands rarely used.

The initial default buttons include:

 Open: Opens an image file previously stored
 Save: Saves the current image
 Save As: Saves the current image to a different name
 Close: Closes the software program
 Print: Prints the current image
 Copy: Copies selected text, selected portions of the current image or the entire image to the clipboard
 Paste: Pastes the current clipboard item onto the screen
 Paste Special: Pastes an overlay of the current item in the clipboard
 Cut: Cut a specific area
 Edit Annotation: Select an annotation to edit
 Text Annotation: Creates text annotation

 Line Annotation: Creates line annotation
 Rectangle Annotation: Creates rectangle annotation
 Ellipse Annotation: Creates ellipse annotation
 Highlighter Annotation: Creates highlight annotation
 Define Image Scale: Calibrates the image to ruler dimensions instead of pixels

ColonyDoc-It Imaging Station 40

 Click the Show Results Window to bring up the colony count results.

 The colony count results for the Petri dish are displayed with tabs on the upper left hand side

of the screen.

 The tabs are Classes, Colonies, Statistics, and Distribution.

 Number of classes in the sample

 Number of colonies in that class

 Percent of colonies of that colony classification in the sample

 Measure Length: Allows users to draw a line and measure the distance between any two points on the

image, units depend on spatial calibration

 Measure Angle: Allows users to draw an angle and measure the degree value contained in that angle
 Measure Area: Allows users to draw an area and measure the area contained within that area
 New ROI: Removes the active Region of Interest and prepares for a new one of the current type
 Rectangular ROI: Changes the current mouse tool to select the Rectangular Region of Interest and brings

up one if already present on the current image

 Elliptical ROI: Changes the current mouse tool to select the Elliptical Region of Interest and brings up one

if already present on the current image

 Polygonal ROI: Changes the current mouse tool to select the Polygonal Region of Interest and brings up

one if already present on the current image

 Freeform ROI: Changes the current mouse tool to select the Freeform Region of Interest and brings up

one if already present on the current image

 Magic Wand ROI: Lets users select a consistently colored area (for example, a red flower) without having

to trace its outline

Reporting Functions

The results of the colony count can be displayed in the results window. To show the results:

Classes

In the Classes tab, information is displayed regarding critical parameters of each class recognized in the Petri dish.
The Classes reported category and associated values are listed below.

NOTE: All dimensional information is reported in pixels unless the plate has been calibrated.

ColonyDoc-It Imaging Station 41

 Total area of the class on the sample (in pixels)

 Percentage of area of the class on the sample

 Mean area of the class (in pixels)

 Standard deviation of the area

 Minimum area (in pixels)

 Maximum area (in pixels)

 Class number

 Total area of that colony (pixels)

 Perimeter of the colony (pixels)

 Average diameter of the colony (pixels)

 Circularity of the colony (numerically depicts roundness of the colony)

Colonies

In the Colonies tab, information is displayed regarding critical parameters of each colony counted in the Petri dish.
The Colonies reported category and associated values are listed below.

NOTE: All dimensional information is reported in pixels unless the plate has been calibrated.

Statistics

In the Statistics tab information is displayed which shows the Statistical property and the area (in pixels)
associated with that property.

NOTE: All dimensional information is reported in pixels unless the plate has been calibrated.

ColonyDoc-It Imaging Station 42

 Minimum area (pixels)

 Colony with the minimal area

 Maximum area (pixels)

 Colony with the maximum area

 Range of area values (pixels)

 Mean of area values (pixels)

 Standard deviation of values

 Sum of all values (pixels)

 Number of colonies

The drop down menu allows users
to report graphical information about
the average diameter, area,
perimeter, and circularity of the
colonies counted in the Petri dish.

Users may also change the number
of bins that display in the graph. (A
bin number of 50 is represented
here)

In the second window, the Property is listed alongside the Area. Several numerical values are listed which include:

Distribution

In the Distribution tab, colony area information is displayed graphically.

Exporting to Excel

To export data, from Colony count results window go to File > Send results to Excel. Save the file in Excel
format to later open the file.

The first tab shows Classes.

ColonyDoc-It Imaging Station 43

The second tab shows Colonies.

The third tab shows Statistics.

ColonyDoc-It Imaging Station 44

Note:

While software from UVP, LLC is an essential tool for assisting an organization to maintain CFR
compliance, UVP cannot claim that this is the only tool needed to achieve overall CFR compliance. The
organization must establish policies and procedures that work in conjunction with such efficient tools, to
ensure total compliance with 21 CFR Part 11 regulations.

 Open the image in question.

 Right click on the image and select

Image Information. Open the History
tab.

 Events are listed in the left column.

Click on each event to view the entry
details on the right.

 Add notes to each event if required.

Supporting 21 CFR Part-11 Compliance

Purpose

US - Food and Drug Administration (US-FDA) created and released Part 11 of Title 21 of Code of Federal
Regulations (CFR) in August 1997.

The rules delineate the conditions under which the US-FDA considers electronic records and electronic signatures
equivalent to paper records and paper signatures. The instructions for compliance really span the entire

organization and its practices. LS software by UVP is one piece that rightly fits into the bigger picture and supports

compliance.

Features

UVP provides software support for the following two sections of CFR regulations:

 Section 11.10 (e) – For electronic records, this section requires the use of computer- generated, time-

stamped audit-trails to track changes.

 The software keeps track of all changes that affect image-data. Any action in the software that modifies the

original data of an image open in the LS workspace, is logged. The log of such changes is individually
maintained for each image and is referred to as „History‟ in the software.

 Section 11.3 (b) (4) – This section mandates that the system be controlled by users responsible overall for

contents of electronic records required to track.

The software provides an elaborate system of maintaining secure user accounts. Assign unique usernames and
passwords to all the users who will be using the software. Each account can also be configured to provide read or
modify access to other users‟ data. Events generated in the audit trail (above) are logged with the username.

Usage

View an Audit Trail (History)

ColonyDoc-It Imaging Station 45

 Open the image for which an Audit

Trail print copy is needed.

 Go to Tools > Reports. (This option

is disabled, if no printer is available.)
A window opens with various types
of reports available.

 To select to print an Audit Trail, click

the Image History item. If other
reports are required, click in the
checkbox of the other reports
needed. For example, if both an
audit trail and the image report need
to be printed, click on Image Report
and Image History.

 Adjust the header and footer settings

or printer settings if necessary, and
print the trail.

Remove the four brass
thumbnuts on the filter box
and remove the filter box
from the housing.

Clean both sides of the
diopter. Remove the filter if
necessary to access the

diopter (refer to Installing
the Filter for instructions on

removing the filter.)

Print an Audit Trail (Image History)

Servicing the ColonyDoc-It

Cleaning and Care

Use 70% Isopropanol Alcohol to clean the ColonyDoc-It external surfaces, base, and doors.

Clean the ColonyDoc-It twice a day, before and after every use.

Cleaning the Diopter

Weekly clean the diopter with a soft photographic lens cleaning cloth dampened with lens cleaning solution.
CAUTION: Do not pour the solution directly onto the diopter.

The diopter is located in the filter box. To access the diopter:

ColonyDoc-It Imaging Station 46

Once the software loads, the Camera control
window should become active. (The user
should be able to select plate diameter sizes,
colony sizes, and use all the functions within the
Camera control window.)

If the Camera control is not active, turn the
power switch off and then back on in the back of
the unit. If a window appears such as the one to
the right, select Cancel.

Replacing Switches

Follow these steps to replace the light switches on the cabinet. Refer to replacement parts for ordering information.

NOTE: This only applies to the light switches on the front of the system. Removal of other switches voids the
manufacturer‟s warranty.

 Unplug the cabinet from the power source prior to removing the power switch.

 To remove the switch from the unit, use a thin flathead screwdriver to pry the switch out from the housing.

Be careful not to scratch the paint of the unit in the process.

 Once the switch is removed, a number of connector wires will be observed plugged onto the back of the

unit. Normally there are two black and two white wires, with some exceptions. Pull one wire out of the old
switch and put it into the same connector location on the new switch. Continue this process for each wire
until all are connect to the new switch.

 Push the new switch into position.

Replacing Fuses

Fuses are located in the back of the unit.

 Remove the fuse by using a flathead screwdriver to turn the fuse counter clockwise.

 Pull the fuse out.

 Insert the new fuse.

 Use a screwdriver to turn the fuse clockwise to lock.

Ordering Replacement Parts and Accessories

Contact UVP or authorized distributor for replacement parts. For replacement parts or components not shown here,
please call UVP Customer Service or place of purchase.

Replacement Parts Part Number Qty Required

Switch, light 53-0135-01 1

Fuse, 3.15AMP/250V 5x20m, SLO BLO 56-0022-04 2

Thumbnut 62-0117-01 Order as required

GFP Filter 38-0340-01 1

Troubleshooting

Camera not active

ColonyDoc-It Imaging Station 47

If the window is still inactive, remove the USB cable from the USB port on the computer and then plug the USB
cable back into the USB port on the computer.

If the window is still inactive, contact Technical Support.

Count not accurate

The user may add, delete, merge, and split colonies for a more accurate count.

The user may increase or decrease the count area by using the ROI tool to change the area of interest using the
Automated or Manual Count.

The user may perform a manual count. Refer to the Manual Colony Counting procedures in this manual.

The user may change the pre-defined filter settings. These settings are area of the colony, perimeter of the colony,

average diameter of the colony, and circularity of the colony. Refer to the manual section Changing Filter Settings.

Preview out of focus

If the preview image is out of focus, select Focus Preview from the Camera control module. If the camera is still
out of focus select Calibrate & Lock Focus from the Camera control module.

No power to the cabinet

Recheck main power cord connections to the system and the wall power (surge protector).

Check the power switch on the back of the unit. Make sure it is in the I position.

Check the fuse located on the main power port. Replace if necessary. If the system continues to blow fuses, call
UVP Technical Support Department.

Return Service Procedure

A Returned Goods Authorization (RGA) number must be obtained from UVP‟s Customer Service prior to
returning any product.

 All returns must be authorized by UVP whether for credit, warranty replacement or repair.

 Items returned for credit may be subject to a restocking charge.

 Please contact our Customer Service Department for a Returned Goods Authorization (RGA).

 No credit will be issued or allowed until UVP has had sufficient time to inspect the product and determine

corrective action.

 Returns must be made within 30 days of issuance of the RGA number and product must be in original

packaging with all manuals and instructions.

 RGA number is non-transferable and good for one use only.

 Products returned for credit or replacement must be in like-new condition. All products must be free from

Bio-Hazardous contamination with a contamination-free certificate attached. Contaminated products will be
returned collect.

 Products returned for repair will be evaluated by Quality Control. Estimated cost for repair will be submitted

to customer for approval. If accepted, all evaluation costs will be credited towards entire repair. Non­repaired products can be returned at customer‟s cost.

 Freight must be prepaid on goods returned to UVP by the customer.

For complete terms and conditions, contact UVP.

ColonyDoc-It Imaging Station 48

If in North America, South America, East Asia or
Australia:

If in Europe, Africa, the Middle East or
Western Asia:

Call [phone] or [phone], and ask
for Technical Support during regular business
days, between 7:00 am and 5:00 pm, PST.

Call [phone], and ask for
Customer Service during regular business

days between 9:00 am and 5:30 pm.

E-mail your message to: [e-mail] or
[e-mail]

E-mail your message to: [e-mail]

Fax Technical Support at [phone]

Fax Customer Service at

[phone]

Write to: UVP, LLC 2066 W. 11th Street,
Upland, CA 91786 USA

Write to: Ultra-Violet Products Ltd. Unit 1,
Trinity Hall Farm Estate, Nuffield Road,
Cambridge CB4 1TG UK

Technical Support

UVP offers expert technical support on all of our products. If there are any questions about the product‟s use,
operation or repair, please contact our offices at the locations below.

Warranty

UVP, LLC warrants all of its products (except tubes, grids and filters which is 90 days) to be free from defects in
material and workmanship for a period of one (1) year from the date of purchase. All transilluminators carry a two
(2) year warranty. The foregoing warranty of UVP shall be of no force and effect if the buyer has modified or
damaged the product.

All warranties or merchantability and fitness for any purpose, and all other warranties, express or implied, except
those expressly set forth herein, are deemed waived and excluded.

UVP's duty under the warranty is limited to replacement and/or repair of the defective part at the option of UVP,
FOB, Upland, California. UVP shall not be liable for any expenses or damages incurred by purchaser except as
expressly set forth herein, and in no event shall UVP be liable for any special, incidental or consequential damages
of any kind.