ColonyDoc-It™ Imaging Station Instruction Manual UVP, LLC Ultra-Violet Products Ltd. 2066 W 11th Street, Upland, CA 91786 Tel: (800) 452-6788 / (909) 946-3197 Fax: (909) 946-3597 Email: info@uvp.com Unit 1, Trinity Hall Farm Estate Nuffield Road, Cambridge CB4 1TG UK Tel: +44(0)1223-420022 / Fax: +44(0)1223-420561 Email: uvp@uvp.co.uk Web site: uvp.com 81-0294-01 Rev.
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”).
ColonyDoc-It Imaging Station 4 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.
ColonyDoc-It Imaging Station 5 Table of Contents Introduction ............................................................................................................................................................................... 7 Components ............................................................................................................................................................................. 7 System Requirements................................................................
ColonyDoc-It Imaging Station 6 Usage ....................................................................................................................................................................... 44 Servicing the ColonyDoc-It ..................................................................................................................................................... 45 Cleaning and Care.........................................................................................................
ColonyDoc-It Imaging Station 7 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.
ColonyDoc-It Imaging Station 8 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.
ColonyDoc-It Imaging Station 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.
ColonyDoc-It Imaging Station 10 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.
ColonyDoc-It Imaging Station 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.
ColonyDoc-It Imaging Station 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.
ColonyDoc-It Imaging Station 13 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.
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.
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.
ColonyDoc-It Imaging Station 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.
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.
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.
ColonyDoc-It Imaging Station 20 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.
ColonyDoc-It Imaging Station The new window will display the Total colonies counted. Fluorescent Colony Counting 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.
ColonyDoc-It Imaging Station 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 Zone Analysis Zone analysis provides users with zone sizing information useful for applications such as inhibition zone analysis. 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.
ColonyDoc-It Imaging Station 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 zones of interest in the Petri dish.
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.
ColonyDoc-It Imaging Station 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 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.
ColonyDoc-It Imaging Station 28 Renumbering Colony/Zone Values 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.
ColonyDoc-It Imaging Station 29 Spiral Plate Counting 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.
ColonyDoc-It Imaging Station 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.
ColonyDoc-It Imaging Station 31 Editing Colonies Add Colonies 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.
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. Delete Colonies Users may delete colonies after performing the initial count (Automated Count, Manual Count, or User Defined Template Count), and deleting colonies manually.
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. Deleted Colony Manual Split Colonies 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.
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.
ColonyDoc-It Imaging Station 35 Merging Colonies 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.
ColonyDoc-It Imaging Station 36 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. To set new filter parameters, click onto the Show Results Window > Filter > Filter class and drag the pointer to the filter class to change.
ColonyDoc-It Imaging Station 37 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 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.
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.
ColonyDoc-It Imaging Station 40 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 curre
ColonyDoc-It Imaging Station 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) 41 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.
ColonyDoc-It Imaging Station 42 In the second window, the Property is listed alongside the Area. Several numerical values are listed which include: 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 Distribution In the Distribution tab, colony area information is displayed graphically.
ColonyDoc-It Imaging Station The second tab shows Colonies. The third tab shows Statistics.
ColonyDoc-It Imaging Station 44 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.
ColonyDoc-It Imaging Station Print an Audit Trail (Image History) 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.
ColonyDoc-It Imaging Station 46 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.
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.
ColonyDoc-It Imaging Station 48 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. If in North America, South America, East Asia or Australia: If in Europe, Africa, the Middle East or Western Asia: Call (800) 452-6788 or (909) 946-3197, and ask for Technical Support during regular business days, between 7:00 am and 5:00 pm, PST.
