Uvp Doc-It Life Science Manuale Utente

81-0328-01 Rev B Doc-It® Life Science Software Installation and User Instructions Doc-It®LS Image Acquisition Software Doc-It®LS Image Analysis Sof

Introduction 5 This system of usernames and passwords is separate from the one that is used to login to the computer. Setting up user accounts is

Performing Colony Counting 95 section of this manual for instructions on creating templates. Click Finish to exit the manual count mode. The softw

Performing Colony Counting 96 Delete Colonies Users may delete colonies after performing the initial count. To delete colonies, ensure that the

Performing Colony Counting 97 Merging Colonies Users may merge colonies after performing the initial count. Colonies should be merged when one colo

Performing Colony Counting 98 In the Spiral Plate Analysis window move the Overlay Size slider bar to the left (to decrease the grid size) or to th

Performing Colony Counting 99 Click OK. If using the software for the first time, no templates are created and the User Defined Template Count op

Performing Colony Counting 100 Statistics In the Statistics tab of the Show Results window, information is displayed which shows the Statistical p

Printing Reports and Images 101 Printing Reports and Images Printing Image Information File Print Command Exporting and Printing Colony Count Re

Printing Reports and Images 102 Print Images can be printed to any Windows-supported printer, regardless of it being a file-printer, local printer or

Supporting 21 CFR Part 11 Compliance 103 Supporting 21 CFR Part 11 Compliance Purpose US - Food and Drug Administration (US-FDA) created and released

Supporting 21 CFR Part 11 Compliance 104 opens with various types of reports available. To print the Audit Trail, click the Image History item. To

Introduction 6 Enter a password. On initial installation, a screen will pop up to request a password and password confirmation. A password is requi

Glossary 105 Glossary Artifact: In imaging, a flaw caused either by the imaging process or by the hardware itself. For example, dust on the camera len

Glossary 106 Pseudocolor: Artificial application of color to a non-color (monochrome) image, or artificial re-tinting of a colored image. Doc-It prov

Introduction 7 Users Rights Depending on the privileges for the user that has logged onto windows, the following rights are available to that user fo

Introduction 8 License Agreement End User License Agreement PLEASE READ THE FOLLOWING AGREEMENT CAREFULLY This Agreement is between UVP, LLC of 2066

Introduction 9 Limited Warranty and Disclaimer Licensor warrants the software and related documentation to be free from defects in materials and work

Navigating the Software 10 Navigating the Software Main Window - Shows the full software screen Menus - Discusses the menus available Toolbars -

Navigating the Software 11 NOTE: Although most commands appear on the menus, some features are only available through the Plug-in Modules. If the Plu

Navigating the Software 12 Cut: Cuts a specific area Undo: Reverses the last command Redo: Repeats the last command Arrow: Selects an ann

Navigating the Software 13 Rearranging Toolbars The order of the individual toolbar sections can be rearranged by placing the mouse arrow over the do

Navigating the Software 14 Showing the Image in Actual Size To show the image in actual size (no scaling), choose View > Zoom. Set the zoom factor

i Table of Contents Introduction...

Using Plug-In Modules 15 Using Plug-In Modules Overview The plug-in modules in LS allow the user to position modules on the work area for easy access

Using Plug-In Modules 16 Positioning Plug-in Modules Rearranging Plug-in Modules Plug-in Modules can positioned anywhere on the screen. Plug-ins c

Using Plug-In Modules 17 The center arrows console allows positioning of the plug-in module at the top, bottom, left or right of an empty workspace b

Using Plug-In Modules 18 If a sample is to be observed over a period of time it is required to snap multiple pictures at regular and definite tim

Using Plug-In Modules 19 Plays the sequence with a number of images to skip in reverse order. The number of images to skip can be set in the Options

Using Plug-In Modules 20 The other two ways this action can be initiated is: If the player is open, click on Extract from the player. If the pl

Using Plug-In Modules 21 Cancel: Closes the window and cancels the process. Saving .AVI Files If files need to be shared with another researcher

Using Plug-In Modules 22 Slide the Brightness control either left or right, or type a desired brightness value into the Brightness text box to the

Using Plug-In Modules 23 Invert Image Select the Invert check box. To stop inverting the image: clear the Invert check box Inverted Image Return to

Using Plug-In Modules 24 Y axis: The horizontal axis. X axis: The axis coming out of the plot, towards you. The plot can also be rotated by drag

ii Overview ...

Using Plug-In Modules 25 Go to View > Plugins to load the Zoom/Pan plug-in. Using Zoom In or Out Click on Zoom In or Zoom Out (located below

Camera Plug-In 27 Camera Plug-In The camera capture plugin provides camera controls for all Canon digital color cameras. To open the capture tab, g

Camera Plug-In 28 Template: This button allows users to define templates to save customized setting and displayed features. Set-Up Canon Capture T

Camera Plug-In 29

Capturing Images 30 Capturing Images This topic discusses the process of capturing images using LS software. The following sections explain the proce

Creating Templates 31 Creating Templates Set-Up Templates Templates enable users to configure specific settings along with unique designator name to

Creating Templates 32 selected. If a setting (or group of settings) is not excluded, it can be overridden on the Canon Camera plug-in before each cap

Creating Templates 33 Click on the Count button to proceed to the Step 2 of 2: Finish tab. If the shape and size sliders are changed to capture a

Editing Images 34 Editing Images Overview Undo and Redo Copy Paste and Paste Special Using Selection Tools (Region of Interest Tools) Overvi

iii Navigating 1D Analysis ...

Editing Images 35 Paste This command takes an image from the clipboard and imports it into the software, displaying it in a new Image window. Note:

Editing Images 36 Using the Region of Interest Tools Using the Selection Tools These tools allow users to mark part of the image for use in other

Using Image Filters 37 Using Image Filters Overview Filter Navigation Image Filter Background Correction and Subtraction Overview LS Software

Using Image Filters 38 Geometry Filters Rotate: Rotates the image around its center, useful for aligning images taken with a crooked gel. Align:

Using Image Filters 39 Burn Changes to a New Image The Burn Changes to a New Image command takes all the changes made to the image and creates a dup

Using Image Filters 40 Flip Vertically This image filter mirror-images an image, top for bottom. Unlike most image filters, it does not degrade the i

Using Image Filters 41 Click onto Sharpen from the Filters plug-in or use the Image > Filters > Sharpen command. Sharpening a large image may

Using Image Filters 42 Viewing Image History Each material change to an image is tracked in LS software s Image History feature. Material changes inc

Using Image Filters 43 measurement value. Right click on the new measurement annotation displayed to change the appearance of the annotation. If d

Using Image Filters 44 Tip: Paste Special also is available from the Toolbar and the Image window's shortcut menu. If the incoming image is

iv Printing Image History...

Using Image Filters 45 To Enter Notes Display the Image Information window as described above. In the Properties tab, type information into the N

Using Image Filters 46 SYPRO Orange: Mimics the colors that appear with a SYPRO Orange stain. SYPRO Red: Mimics the colors that appear with a SYP

Using Image Filters 47 Tip: There is little point to increasing an image's size, although the filter does support it. Such an image would have

Using Image Filters 48 Align an Image Align tool rotates the grid overlaid on the image so that it can be aligned with vertical/horizontal features

Using Image Filters 49 Scan an Image from a Scanner Select Image > Scan > Start Scanning. Change any settings offered by the device as desi

Using Image Filters 50 down list) first. For example, if the sample width of the image is 500 cm, select centimeters. Type the number of metric uni

Annotations 51 Annotations Overview Annotations allow users to notate areas of an image without changing the image itself. This means that areas in th

Annotations 52 Ellipse: Ellipse annotations are very similar to Rectangle annotations except that they are oval rather than rectangular. Select the

Annotations 53 Click OK. Selecting Annotations After creating an annotation, select it either to change formatting properties or to graphically mov

Annotations 54

Introduction 1 Introduction Welcome Life Science (LS) software from UVP lets users acquire, enhance, and analyze images in a simple and efficient wa

Annotations 55 Formatting Annotations The Annotation Formatting menu contains options to format a selected annotation. Change the formatting of an a

Annotations 56 Creating Annotations Creating a Text Annotation Select Tools > Add Annotation > Text. Click the position on the image to

Loading and Saving Images 57 Loading and Saving Images Loading Images LS Software will load images in popular formats, including JPEG, TIFF, GIF, PNG,

Loading and Saving Images 58 To Save Using a Different File Folder, Name or Type From the File menu choose Save As. The Save window will appear.

Loading and Saving Images 59 compression formats. By comparison, a lossless format does not store as compactly, but also does not change the image in

Performing 1D Analysis 60 Performing 1D Analysis Navigating 1D Analysis 1D Analysis Image Windows Features 1D Analysis Context Menu Commands 1

Performing 1D Analysis 61 Find Lanes and Bands: Searches for lanes and bands in the image. Edit Objects: Select, move and resize lanes, bands,

Performing 1D Analysis 62 1D Analysis Context Menu Commands The 1D Analysis context menu appears when 1D objects (lane, band, etc) are selected in t

Performing 1D Analysis 63 From the 1D Analysis toolbar menu or plug-in, click on Find Lanes and Bands. The Lanes/Bands dialog window appears and a

Performing 1D Analysis 64 On the Find Lanes and Bands window click Use auto-detected parameter values. The original parameters will be restored and t

Introduction 2 Minimum System Requirements Windows XP Professional with Service Pack-2 or higher (32 bit only), Vista (32 bit only), or Windows 7

Performing 1D Analysis 65 1D Analysis Settings To access analysis settings, go to Analysis > 1D Analysis > Settings > 1D Analysis tab. Th

Performing 1D Analysis 66 Move the cursor over the image. A movable horizontal line will appear whenever the cursor is moved over a lane. Simply mo

Performing 1D Analysis 67 Place the mouse hand over the top or bottom of the band's extents and click and drag the box border to increase or t

Performing 1D Analysis 68 From the Analysis > 1D Analysis > Master Tools, click on Delete All Analysis Data or go to the 1D Analysis plugin &

Performing 1D Analysis 69 In this window, the software allows users to perform various changes to the lane including: Name Geometry Band Prope

Performing 1D Analysis 70 Display Multiple Lanes The software has two options for displaying a multiple lanes. To Display Multiple Lanes by Selecting

Performing 1D Analysis 71 Underneath the graph and the lane image, in the Display options section, the following are available: Band Peaks: Select

Performing 1D Analysis 72 Viewing Data Explorer Results Printing Data Explorer Reports Exporting Data Fixed Image and Analysis Reports Overv

Performing 1D Analysis 73 When selecting theses reports notice the various fields being selected/deselected from the list of data fields. Select from

Performing 1D Analysis 74 I-Max: Maximum intensity value reached within a lane. It actually shows the brightest (for black background) or darkest (

Introduction 3 On the Fly Activation To immediately activate the software through the Internet: Choose On the fly activation. If the computer is

Performing 1D Analysis 75 Reading the chart: The chart is read like a matrix, each cell value representing the computed/calibrated value for that b

Performing 1D Analysis 76 o To Excel o To CSV Click the To Excel or To CSV button. Name the file and click Save. Select a Report Type Summa

Performing 1D Analysis 77 The Analysis Bands Report: Band Name and ID Calculated peak values (Rf value and molecular weight); Intensity of the

Performing 1D Analysis 78 Background correction is necessary to account for possible variable illumination or overexposure during image capturing,

Performing 1D Analysis 79 and quite distinct. Joined Valleys requires a sensitivity value to be entered. A higher value of sensitivity starts "

Performing 1D Analysis 80 Graph display and units are easily modifiable by the user. The user may change the unit type or change the colors of the b

Performing 1D Analysis 81 Click Edit. The Edit window pops up. Change the concentration value to the desired number. Click OK. Deleting Data

Performing 1D Analysis 82 Note: Moving the bands or resizing them also changes their net intensity values. As a result, the user will see the word &q

Performing 1D Analysis 83 Molecular Weight Calibration Calibration of molecular weight (MW) involves associating a known standard with one or more

Performing 1D Analysis 84 In the Step 1: Select MW standard tab select the standard to copy. Then click on Copy. The Edit window will appear. Cha

Introduction 4 Offline Activation Select Offline Activation if the computer is not connected to the Internet. This allows the user to obtain the ac

Performing 1D Analysis 85 Using Manual Placement of Weights If the user does not want to use the Stretch Factor, the weights can be adjusted individu

Performing 1D Analysis 86 Retardation factor (Rf) Lines Automatic Rf Line Determination When two or more lines are calibrated with molecular weight

Performing 1D Analysis 87 are red marks on the Rf line created, the Rf line will not be created when Confirm Add is selected. Ensure that the entire

Performing 1D Analysis 88 Overview Dendrograms are graphical/numerical displays used to show the similarity bands. The similarity is grouped into cl

Performing 1D Analysis 89 Creating clusters Initially, each lane has its own cluster. Then, repeatedly, a linkage rule (see below) is used to merge

Performing 1D Analysis 90 http://marketing.byu.edu/htmlpages/books/pcmds/WARD.html Neighbor joining: At each stage of clustering the total branc

Performing Colony Counting 91 Performing Colony Counting The software offers several functions for counting colonies. Automatic Counting Manual Co

Performing Colony Counting 92 a line through the colony to be split o Auto Split Colonies – Allows users to split colonies by clicking on a colony t

Performing Colony Counting 93 Circle Radius To change the circle radius, click the drop down arrow and select from the numbers to change circle pixel

Performing Colony Counting 94 Manual Counting Step 1: Select Classes The window that appears after choosing Manual Count is the manual count windo