Bio-rad Model 680 Microplate Reader Accessories Manual do Utilizador

P/N 4000138-03 RevA Bio-Rad Laboratories Life Science Group 2000 Alfred Nobel Drive Hercules, CA 94547 VVeerrssiioonn 55..22 UUsseerr GGuuiid

Microplate Manager User Guide 2 Figure 1. Workflow of Microplate Manager Microplate Manager can perform three general types of microplate rea

Microplate Manager User Guide 92 Figure 68. Analysis Settings in the BSE Screening Report. You can change the constants for k1, k2, and/or k3 to mo

Chapter 6. Data Formatting and Reports 93  Each custom report template is released as a controlled document with its own part number and revision l

Microplate Manager User Guide 94 Each sample well shows the result (POS, NEG, or ???) and absorbance value. Wells flagged with a “*.***” are out of r

Chapter 6. Data Formatting and Reports 95 Figure 73. Example of a Raw Image Report (1536-well plate).  Kinetic Protocols will create multiple im

Microplate Manager User Guide 96 Figure 74. Image menu. The image is displayed in a window that can be resized by dragging the lower right corner o

Chapter 6. Data Formatting and Reports 97 addition, if applicable, the assay number, well formatting, and current value of the well are displayed in

Microplate Manager User Guide 98 Show Pattern on the IMAGE menu displays the area of the well used for data collection (i.e., the extraction area). T

Chapter 6. Data Formatting and Reports 99 Figure 76. Raw Data Report. For absorbance readings, the Raw Data Report will contain the absorbance val

Microplate Manager User Guide 100  This report will be unavailable if you elected to ratio the results of a dual wavelength reading in the Protocol.

Chapter 6. Data Formatting and Reports 101 Figure 78. Velocity Report. The Velocity Report displays the velocities of your well readings, based on

Chapter 1. Introduction 3 template for your microplate. Finally you take the reading. If you want to use the particular Protocol you’ve created agai

Microplate Manager User Guide 102 The Adjusted Velocity Report displays the adjusted velocity for each well calculated by subtracting the mean veloci

Chapter 6. Data Formatting and Reports 103 Figure 81. Kinetic Standard Errors Report. The Kinetic Standard Errors Report shows the calculated stan

Microplate Manager User Guide 104 Figure 82. Kinetic Plots Report. The Kinetic Plots Report displays plots of the changes in absorbance with time o

Chapter 6. Data Formatting and Reports 105 Figure 83. Kinetic Zoom Plot. This window shows additional velocity information for a single well. It d

Microplate Manager User Guide 106 Figure 84. Define Labels dialog box. You can specify up to six different labels. There are four predefined labels

Chapter 6. Data Formatting and Reports 107 Fill Labels After you have created a label, you can enter the information to be included in that label im

Microplate Manager User Guide 108 Figure 87. Editing raw data. Your data will be displayed in a spreadsheet format. To change a particular number,

Chapter 6. Data Formatting and Reports 109 With your data displayed, select Edit Outliers... from the EDIT menu. This will open the Select Outliers

Microplate Manager User Guide 110 Editing or Replacing the Template in a Data File After a Protocol has been run, the template from the Protocol File

111 7. Printing and Exporting This chapter describes Microplate Manager’s functions for printing reports and exporting data. Printing All the reports

Microplate Manager User Guide 4 Data Files Data Files contain the data from a microplate reading. They have the extension .mpm. For an Endpoint readi

Microplate Manager User Guide 112  To automatically print reports immediately after a reading has been performed, click on the Reports... button in

Chapter 7. Printing and Exporting 113 To export, with your template or text-based data window open, select Export... from the FILE menu. From the Sa

Microplate Manager User Guide 114 Kinetic Data Formats COL Format The column format consists of (4 + (# of rows) * (# of cols)) lines. Line 1: “Col”

Chapter 7. Printing and Exporting 115 Line ((reading# - 1)*(# of rows + 2) + row# + 4): <row1:col1><tab><row1:col2><tab>...

117 8. Quick Guides Creating a New 96-Well Template See Chapter 5 for details. 1. Choose New Template > 12 x 8 from the FILE menu. 2. Click on the

Microplate Manager User Guide 118 a. Select Standard Curve Report or Unknown Concentration Report from the VIEW menu. b. Use the tabs to select the

Chapter 8. Quick Guides 119 5. Click Analysis Options to set the Kinetic analysis parameters. 6. Save the Protocol by choosing Save Protocol or Sav

Microplate Manager User Guide 120 6. Save the Protocol by choosing Save Protocol or Save Protocol As... from the FILE menu. 7. Initiate the Protoco

Chapter 8. Quick Guides 121 Creating and Running a New Endpoint Protocol with a New Template See Chapters 4 and 5 for details. 1. Select New Endpoin

5 2. Installation and Setup Instrument Specifications Computer Microplate Manager software is compatible with Windows® 95, 98, ME, NT, 2000, and XP.

Microplate Manager User Guide 122 Creating and Running a Multiple Plate Protocol with a Stored Template See Chapter 4 for details. 1. Select New Mult

Chapter 8. Quick Guides 123 Creating and Running a New Multiple Plate Protocol with a New Template See Chapters 4 and 5 for details. 1. Select New M

Microplate Manager User Guide 124 8. At the end of the run, save the data by choosing Save Data/Template or Save Data/Template As... from the FILE m

125 Appendix A. Menus The pulldown menus in Microplate Manager change depending on the particular part of the application you are using. For example,

Microplate Manager User Guide 126 Close closes the current file. All windows associated with the current file are closed. If the file has been modifi

Appendix A. Menus 127 Edit Standard Conc... opens a form in which you can enter concentrations of standards. Edit Outliers... opens a dialog box in

Microplate Manager User Guide 128 Format This menu is available only when a template is active: Assay changes the pointer to a tool for defining the

Appendix A. Menus 129 External Standards... opens a dialog box in which you can select another file from which to import standards to be used in cal

131 Appendix B. Glossary Assay: A set of wells grouped together for analysis. Blank: A well used for background subtraction. Endpoint analysis: Analy

Microplate Manager User Guide 6 Connecting the Microplate Readers to the Host Computer A serial cable is required to connect the Benchmark Plus, Benc

133 Appendix C. Ordering Information The following products can be ordered from Bio-Rad: Catalog Number Product Description 170-9520 Microplate Man

135 Appendix D. Warranty Bio-Rad Laboratories warrants that the Microplate Manager software shall substantially conform, in all operational features,

Microplate Manager User Guide 136 this manual and the software program contained herein may not be copied, in whole or in part, without the prior wri

137 Index Assays Annotating, 64 Defining, 62 Editing, 64 BSE Screening Report, 90 Computer and operating system requirements, 5 Concentrations Standa

Microplate Manager User Guide 138 Exporting data, 46 Plate loading, 44 Ratio delay, 49 Saving data, 46 New features, 4 Outliers, identifying, 108 Pag

Index 139 Scan Well command, 29 Scenarios, 16 Standard curves Comparing external and internal, 86 Displaying, 82 Standards, external Description, 75

141

Chapter 2. Installation and Setup 7 C:\Program Files\Bio-Rad\Microplate Manager. You can select a different directory when prompted to do so by the

9 3. Getting Started Menus, Toolbars, and Other Features Menu Bar Microplate Manager has a standard menu bar with pulldown menus that include all the

Microplate Manager User Guide 10 Right-click Commands You can access many of the commands associated with the action you are currently performing by

Chapter 3. Getting Started 11 Selecting a Reader To select an instrument, go to the FILE menu and select Select Reader. Figure 5. Select Reader di

ii Catalog Number 170-9520 Bio-Rad Technical Services Department Open Monday–Friday, 8:00 a.m. to 4:00 p.m., Pacific Standard Time. Phone: (800) 4

Microplate Manager User Guide 12 Ultramark and Ultramark EX Setup With a Protocol window open, select Instrument Setup from the FILE menu. Figure 6

Chapter 3. Getting Started 13 Figure 7. Model 550 Setup dialog box. For each filter, enter the appropriate wavelength in the dialog. The wavelengt

Microplate Manager User Guide 14 In the Preferences dialog, enter or select the Default File Location for opening and saving files, and enter or sele

Chapter 3. Getting Started 15 Figure 9. Examples directory. Clicking on any of these Data Files will open Microplate Manager and display the templ

Microplate Manager User Guide 16 Importing Data This version of Microplate Manager will read files from the previous version (5.0.x). Tab-delimited a

Chapter 3. Getting Started 17 Scenario 1. Endpoint Assay with Previously Formatted Template You want to perform an Endpoint assay using a template

Microplate Manager User Guide 18 Concentration Report from the VIEW menu). You select Print... from the FILE menu to print this report. You decide th

Chapter 3. Getting Started 19 After inserting your plate into the reader, you click on Run and the reader begins collecting data. At this point, bot

Microplate Manager User Guide 20 Figure 12. Comparing external and internal standards.

21 4. Protocols Protocols contain the settings for controlling the microplate reader. To read a microplate, you must first open a Protocol window and

iii Table of Contents 1. Introduction ... 1 Overview of Microplate Manager...

Microplate Manager User Guide 22  If no reader is found, you will receive a warning message. Make sure the reader is turned on, and check all the co

Chapter 4. Protocols 23 Figure 13. Example of a Protocol dialog box (Ultramark version shown). Each Protocol dialog box has numerous settings for

Microplate Manager User Guide 24 Selecting a Template Each Protocol File includes a microplate template that specifies the number of wells to be read

Chapter 4. Protocols 25 Figure 14. Selecting a plate type (Benchmark Plus types shown). The available plate types are different for the Benchmark

Microplate Manager User Guide 26 or Save Protocol As... from the FILE menu, or click on the Save button on the main toolbar.  Protocols are not auto

Chapter 4. Protocols 27 Figure 17. Measurement wavelength settings in the Protocol dialog box (Benchmark Plus version shown). For the Benchmark Pl

Microplate Manager User Guide 28 Incubator Controls (Not Available for Model 550) To use the incubator in the microplate reader, click on the Incuba

Chapter 4. Protocols 29  In Multiple Plate Protocols, the initial wait time only applies to the first plate in the batch to be read. Mix Settings M

Microplate Manager User Guide 30 Figure 20. Scan Well settings (Benchmark Plus only). In the Scan Well dialog box, specify the Row and Column of th

Chapter 4. Protocols 31 Figure 21. Well Scan Graph (Benchmark Plus only). You can aim your cursor at any point in the graph and display the wavele

iv Setting Filters ... 11 Ultramark and Ultramark EX Setup...

Microplate Manager User Guide 32 Figure 22. Reports dialog box for Endpoint and Multiple Plate Protocols. At least one non-custom report must be se

Chapter 4. Protocols 33 For example, if the labels “Date” and “Operator” are created in a Protocol File, then when that Protocol is run, a dialog bo

Microplate Manager User Guide 34 If you don't fill in the labels, you will be prompted to do so when you run the Protocol. You can also define a

Chapter 4. Protocols 35  Protocols are not automatically saved when you click on Run. To preserve changes to a Protocol File, you must save it. To

Microplate Manager User Guide 36 Figure 26. Features of an Endpoint Protocol dialog box. Absorbance Delay and Ratio Delay Absorbance Delay is ava

Chapter 4. Protocols 37 Figure 27. Absorbance Delay dialog box. In the Absorbance Delay dialog box, click on the Use Absorbance Delay checkbox to

Microplate Manager User Guide 38 Figure 28. Ratio Delay dialog box. Kinetic Protocol Features Kinetic Protocols are used to acquire a series of abs

Chapter 4. Protocols 39 Figure 29. Features of a Kinetic Protocol dialog box. The controls common to all Protocols are described on page 23. The

Microplate Manager User Guide 40 Enter the number of readings you want to take in the Readings column. Next enter the interval between the start of t

Chapter 4. Protocols 41 Figure 30. Analysis Options in the Kinetic Protocol dialog box. The settings in this dialog box will only affect the analy

v Plate Loading in a Multiple Plate Protocol... 44 Saving Files from Multiple Plate Readings...

Microplate Manager User Guide 42 To set absorbance limits, select the appropriate checkbox(es) and enter ODs in the appropriate field(s). Note that i

Chapter 4. Protocols 43 For cases where the absorbances decrease with time, the velocities will be negative. In these cases, select the Negative Kin

Microplate Manager User Guide 44 Figure 32. Features of a Multiple Plate Protocol dialog box. The controls common to all Protocols are described s

Chapter 4. Protocols 45 Without a Plate Loader For readers not connected to a plate loader, enter the number of plates in the Num of Plates field. T

Microplate Manager User Guide 46 From this dialog box you can enter the main Twister control panel by clicking on the Twister Configuration/Training

Chapter 4. Protocols 47 Figure 34. Save Format selections. MPM Format Only Under Save Format, select MPM format only. When you click on Run, you w

Microplate Manager User Guide 48 Figure 35. Multiplate Export Options dialog box. This dialog gives you a number of options for exporting your plat

Chapter 4. Protocols 49 Under Data Labeling, select if and how you want to label the values reported for the wells in a plate. You can export additi

Microplate Manager User Guide 50 Figure 36. Absorbance Delay dialog box. In the Absorbance Delay dialog box, click on the Use Absorbance Delay chec

Chapter 4. Protocols 51 Figure 37. Ratio Delay dialog box.

vi Kinetic Correlation Coefficient Report ...102 Kinetic Standard Errors Report...

53 5. Templates Templates allow you to specify the number and layout of the wells on your microplates. You use this layout information when analyzing

Microplate Manager User Guide 54  It is useful to format your template before reading the microplate so that this information can be included in the

Chapter 5. Templates 55 Benchmark Plus and Ultramark users can select from one of three standard plate types: 12 × 8, 24 × 16, or 48 × 32. Benchmark

Microplate Manager User Guide 56 Figure 39. Creating a custom plate type. In this dialog box, if the template format you want is listed, simply dou

Chapter 5. Templates 57 Figure 40. Defining the format of a plate. In the Define Plate Format dialog box, you can enter the numbers of Columns and

Microplate Manager User Guide 58 Figure 41. Entering the physical dimensions of your plate. In the Physical Dimensions dialog box, you can enter th

Chapter 5. Templates 59 When you have specified the physical dimensions of your plate, click on the OK button. Template Features When you select a n

Microplate Manager User Guide 60 Template Size You can display a template in three sizes. Under the VIEW menu, select Show Full Size, Show Compact, o

Chapter 5. Templates 61 Figure 44. Well Info dialog box. The info box shows the number, type, and reading of the well you selected. It also lists

vii Appendix A. Menus ... 125 Appendix B. Glossary ... 131

Microplate Manager User Guide 62 Figure 45. Format menu and template toolbar. Some additional assay-related commands are located on the EDIT and

Chapter 5. Templates 63 subsequent assays, they appear as different colors. Independent statistical analysis and data reduction are performed for ea

Microplate Manager User Guide 64 Assay Info To rename your assays, annotate them, or change their colors, select Assay Info... from the ASSAY menu. T

Chapter 5. Templates 65 Defining Standards and Unknowns After you have defined the assays in the template, you are ready to identify the wells cont

Microplate Manager User Guide 66 unknown or standard shares the same number, they are part of the same replicate group (see page 68). Clicking on sev

Chapter 5. Templates 67 If your well numbering is out of sequence and you want to correct it, select Resequence Well Names from the FORMAT menu. The

Microplate Manager User Guide 68 Replicate Groups A replicate group is a group of wells with the same standard or unknown. For each replicate group,

Chapter 5. Templates 69 With your Standard or Unknown pointer, enter the number of replicates in each group in the field. Then click on the Autofill

Microplate Manager User Guide 70 desired replicate group from the pulldown list of existing replicate groups within the dialog box. Entering Standard

Chapter 5. Templates 71 Click on the Enter Manually button to directly input the concentrations of your standards. Then type in the concentrations i

Microplate Manager User Guide 72 • Run at least three replicate wells for each dilution of standards and samples. • Run an adequate number of sampl

Chapter 5. Templates 73 Click on the Enter Manually button to directly input the dilutions of your unknowns. Then type in the dilution factor in the

Microplate Manager User Guide 74 Figure 54. External Standards dialog box. If you are already using external standards, the External Standards chec

Chapter 5. Templates 75 Select the Data File containing the external standards and click on Open. The names of all assays with defined standards wit

Microplate Manager User Guide 76 In the Unknown Concentration report, external standards are labeled XS1, XS2, XS3, etc. Saving Templates To save a t

77 6. Data Files and Reports After you have run a Protocol, a Data File is generated and the resulting data is displayed automatically in one or more

Microplate Manager User Guide 78 Limit, Matrix and Normalization Reports The Limit Report, Matrix Report, and Normalization Report allow you to set u

Chapter 6. Data Formatting and Reports 79  For Kinetic data, your limits will be adjusted velocities; for Endpoint data, your limits will be absorb

Microplate Manager User Guide 80 Figure 59. Matrix Report. The Matrix Report is similar to the Limit Report (see previous page), except that the da

Chapter 6. Data Formatting and Reports 81 Figure 60. Normalization Report. The Normalization Report displays absorbance or velocity data for each

Chapter 1. Introduction 1 1. Introduction This manual assumes that you are familiar with your computer and standard commands and functions associate

Microplate Manager User Guide 82 Figure 61. Control Report. The Control Report displays absorbance or velocity data for each well as a percentage o

Chapter 6. Data Formatting and Reports 83 Figure 62. Standard Curve Report. Features of the Standard Curve Display For replicate groups of standar

Microplate Manager User Guide 84 If more than one assay has been defined on your plate, click on the tabs at the top of the window to switch between

Chapter 6. Data Formatting and Reports 85 The polynomial regression models (Linear, Quadratic, and Cubic) and logistic models are examples of global

Microplate Manager User Guide 86 Figure 64. Selecting a transformation method. The equation at the bottom of the window will change based on your t

Chapter 6. Data Formatting and Reports 87 Figure 65. Analysis of Variance box. In the Analysis of Variance dialog box, the key statistics are lis

Microplate Manager User Guide 88 This report also provides statistics for each replicate group of wells, including mean, standard deviation, and coef

Chapter 6. Data Formatting and Reports 89 To change curve fit options or axis types, open the Standard Curve Report (see page 82) and select the des

Microplate Manager User Guide 90 BSE Screening Report The BSE Screening Report is a Microsoft® Excel workbook with built-in calculation functions for

Chapter 6. Data Formatting and Reports 91 Figure 67. BSE Screening Report, generating using Custom Reports. The BSE Screening Report contains two