NucleoView™ User's Guide P/N 991-0006 Ve r sio n 2 .
NucleoView ™ A part of the NucleoCounter ® ™ NC-100 and NucleoCounter ® YC-100 ™system Manual No. 991-0006 (English) Version 2.3 August, 2012 ChemoMetec A/S Gydevang 43, DK-3450 Allerød Telephone: +45 48 13 10 20, Fax: +45 48 13 10 21 Internet: www.chemometec.com, E-mail: Sales@chemometec.
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Customer support If you have questions about installing or using your NucleoView T M software check this user's guide first - you will find answers to most of your questions here. If you need further assistance, please contact customer support at ChemoMetec A/S.
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Intended use Intended use The NucleoView™ software is developed as a dedicated accessory to the NucleoCounter™ NC-100 and the NucleoCounter™ YC-100 instruments; it is intuitive and easy to use. NucleoView™ offers the user several features when connected to the NucleoCo unter™. With NucleoView™, correction for dilution of the samples and calculation of viability becomes easy.
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Table of contents Table of contents 1 INSTALLATION ............................................................................................................ 1 1.1 I NSTALLATION OF THE N UCLEO V IEW P ACKAGE VER . 2.3 - W INDOWS 7 ................................. 2 1.2 R EMOVAL OF THE N UCLEO V IEW SOFTWARE .................................................................... 5 1.2.1 2 4 5 6 TM - Windows 7 .........................................................
Table of contents 6.3 V IABILITY REPORT – P RINT AND EXPORT ...................................................................... 34 6.3.1 6.4 I MPORT DATA INTO E XCEL ....................................................................................... 36 6.4.1 7 R EPORT HEADER .................................................................................................... 40 6.6 D EFAULT SETTINGS FOR N UCLEO V IEW 6.7 C ONFIGURE TEXT EDITOR ................................................
1 Installation 1 Installation When the NucleoCounter is connected to a computer running NucleoView it is possible to register the estimated cell concentration and the collected image of the NucleoCassette chamber. Connecting a NucleoCounter to a computer does not affect the operation of the NucleoCounter in any way and the NucleoView software performs no additional image analysis.
1 Installation 1.1 Installation of the NucleoView Package ver. 2.3 - Windows 7 2 When the computer has been turned on and is finished with the start -up process, insert the USB Flash disk supported with the NucleoCounter to the computer. Let the computer install the USB Flash disk and the open the DISK. Figure 1 NucleoView Package v2.3 Installer located on the USB Flash disk Activate the application “NucleoView Package v2.
1 Installation Figure 3 Installer Setup - Welcome Hit “Next” Figure 4 Installer Setup - Prerequisites Check the check box in Figure 4 Installer Setup - Prerequisites and hit “Next”.
1 Installation Figure 5 Installer Setup – Ready to Install Hit “Install”. Figure 6 Installer Setup – Installing and Windows Security After the actual Installation is started you will be prompted to accept the installation of the device software for the USB driver.
1 Installation In the background the installation continues and when this is over the following dialogue appears. Then hit “Finish”. Figure 7 Installer Setup – Completed The first time a NucleoCounter is turned on while connected to the computer, the computer will identify the NucleoCounter as new hardware and install the drivers for it. So the screen will show the following message. 1.2 Removal and upgrade of the NucleoView software 3 For removal of the NucleoView software follow the directions below.
1 Installation 1.2.1 Removal of NucleoView TM - Windows 7 4 5 To remove the NucleoView software open the NucleoView folder (see Figure 8 Contents of the NucleoView folder (before uninst000.exe is activated).). The folder should be located in the root directory of the local hard disk (C:\Nucleoview) if the location was not changed during the installation. 6 In the NucleoView folder double-click on “uninst000.exe ” and confirm that the NucleoView software is to be uninstalled.
1 Installation 8 Figure 9 Contents of the NucleoView folder (after uninst 000.exe is activated) . If the program has to be removed completely you can just delete the files and folders now. Remember you will loose ALL data, if you delete the contents of the “data files” folder from Figure 9. In case you are upgrading the NucleoView program, DO NOT delete any files or folders after “uninst000.exe” was activated. 1.2.
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2 Getting started with NucleoView TM 2 Getting started with NucleoView TM NucleoView allows the user to register the results of cell counts with the NucleoCounter on a computer. This is useful when documentation of results and data is needed. 2.1 Launch NucleoView TM NucleoView can be activated through the Windows “Start” menu. First select “NucleoView 2.2” from the “Programs” submenu, and then select “NucleoView”.
2 Getting started with NucleoView 2.2.1 TM Viewer (limited access rights) mode The Viewer mode is recommended for installations retrieving and viewing data over a data network – not for collection of data. In this mode it is possible to retrieve and view all data from the CM files received from a NucleoCounter. It is possible to change all settings in the program, but it will not be saved to the files. 2.2.
2 Getting started with NucleoView 4. TM Launch NucleoView again, and you will have the possibility of making the choice of modes again. DO NOT use this procedure to perform regular changes between Viewer and Data collection mode, since it can affect the ability to change parameters in your older files. Only use this procedure if you during initial startup accidentally chose the wrong program mode. 2.2.
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3 The structure of NucleoView TM 3 The structure of NucleoView TM NucleoView is operated through a number of tabs. The different tabs are selected by clicking on the corresponding tab. The tabs are shown in figure 12. Figure 12 The four tabs of NucleoView. The default startup screen is the Measurement tab. For detailed descriptions of the different tabs see the following chapters. An overview of the four different tabs is given below. 3.
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4 Measurement tab 4 Measurement tab Measurement is the default start-up tab of NucleoView. In this tab, data and results transferred from the NucleoCounter are automatically displayed. An example of the Measurement tab is shown in figure 13. Once NucleoView has been launched the Measurement tab is automatically displayed. Usually there are no files in the active session upon start -up. The object intensity histogram is then replaced with a small text box saying, “Please select a valid folder”.
4 Measurement tab 4.1 Concentration of cells in the NucleoCassette TM The estimated cell concentration of the cell lyzate in the NucleoCassette is displayed at the top of the window in a field labeled “Concentration of cells in NucleoCassette”. The cell concentration is given as cells per mL. Most often the cell suspension has been diluted with the Lysis and Stabilizing buffers before the analysis.
4 Measurement tab Figure 14 Data relating to the dilution of the sample. All data regarding the multiplication factor is stored in the individual data file, thus making it possible to keep track of the individual s ettings for each analysis. Once NucleoView has received a new file from the NucleoCounter it automatically saves the default settings for the multiplication factor to the file. The factory set of default settings are: Multiplication factor = 3.0 (Valid range: 1.0 -50000.0).
4 Measurement tab 11 Amount of Stabilizing buffer equals amount of Lysis buffer , this feature is enabled by the default settings. These default settings can be changed in the Utilities tab, see chapter 6.6 Default settings for details. For further description of the multiplication factor and representation of the result refer to the NucleoCounter User's Guide. 4.
4 Measurement tab 4.5 Browse and Today Each day NucleoView is launched in data collection mode, a new session (folder) is created. The folder’s name is the date of the session (yymmdd). When NucleoView is launched in the Viewer mode, no new folder is created. It is possible to browse sessions created at an earlier date in both program modes. When a measurement is performed and data is transferred to the computer, a file containing the measurement data is created.
4 Measurement tab received from the NucleoCounter then NucleoView detects this and changes the active session to the session of the day, displaying the most recent results. The "Today" button will also change the active session to the current days session. If comments have been added to a file this will be shown next to the name of the CM file eg. File 040831-054.CM from figure Figure 15 has the comment “Total Vial 2” and is shown next to the file name. This makes it easy to navigate and locate the files.
4 Measurement tab When NucleoView is unable to change and save the information in the CM -file (e.g. on a computer where NucleoView is installed in the Viewer program mode), a small icon appears left to the path field as shown in Figure 16. Information can be changed but the changes are not saved to the file. Figure 16 Data cannot be saved to the CM-file when the radio button is shown.
4 Measurement tab When CM-files are not from today’s session the “Edit ” button is shown. This button must be activated before changes of the settings can be made, however these changes will only be saved to the CM-file if accessed using the PC that collected the files, and if the files still remain in their original folder. The files cannot be changed from other PCs or if they have been moved from the original folder.
4 Measurement tab axis is signal intensity on a scale from 0 to 255. The unit of the y -axis is the number of stained nuclei or objects. Figure 19 The object intensity histogram. Variation of the background level of the image gives rise to a number of signals of low intensity. These signals are found to the far left of the object intensity hi stogram, generally the intensities of the background signals are below 20.
4 Measurement tab To obtain a copy of the image, use the "Save image " button. This will activate a standard save dialogue where the location and name of the resulting image is defined. The image is saved as a .BMP image, a graphical format, which can be used with variety of common applications, such as word processing software. The size of t he BMP image is 140 KB and it looks as shown in figure 20. Figure 20 Image created with “Save image” button.
4 Measurement tab Figure 21 Resizing the image created using the “Save image” button. Figure 22 Resized image created using the “Save image” button.
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5 Viability tab 5 Viability tab NucleoView offers the possibility of automatic calculation of the percentage and concentration of viable cells. The results can be saved and printed or exported later (see chapter 6 Utilities ). The Viability tab looks as shown in figure 23. The upper and middle parts of the Viability tab consists of data relating to the total cell count and the non -viable cell count, respectively. The results of the viability calculations are found in the bottom of the tab.
5 Viability tab shown immediately. If comments have been added to a file this will be shown next to the name of the CM file. If the first file is selected as the total cell count, no file is automatically selected as the non-viable cell count and only the file list is shown (the information about the file and the results disappear). Select the file that is the non -viable cell count manually and the information about the file and results will be shown.
5 Viability tab The representation of the "Concentration of viable cells" follows the result mode used for the total cell count. However the calculations of Viability and Concentration of viable cells are based on the full precision results from the analyses and not the truncated values, which are present when result mode 2 or 4 are active. Therefore, when the NucleoCounter is set to result mode 2 or 4 the displayed results of the viability calculations may differ from manually calculated results.
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6 Utilities tab 6 Utilities tab In the Utilities tab (figure 26) it is possible to print and export results and viability calculations. Furthermore it is possible to change the information on the header of the prints and exports, and the default settings, which are used when data from the NucleoCounter is received in the Measurement tab. Figure 26 The Utilities tab. 6.1 Report path The report path is found in the top left corner of the Utilities tab.
6 Utilities tab File name Concentration of cells pr. mL in the NucleoCassette (Cells/ml (cass.)) Multiplication factor (MF) Concentration of cells pr. mL in the original cell suspension (Cells/ml (susp.)) Comment Operator On the top of the result list a header is printed. The header consists of the location , and name of the exported file is printed path is printed, company information, address, department, NucleoCounter serial no.
6 Utilities tab 3. When the appropriate files has been selected, click “Continue” and the files will be printed or exported. If many files are printed or exported it can take a few minutes. For an example of a printed result list, see Appendix 1: Printed result list. When files are exported a message box appears, see figure 28. The message box shows the location and name of the exported files. Figure 28 The message box displayed when files are exported.
6 Utilities tab imported into e.g. MS Excel (see chapter 6.4 Import data into Excel). The files are tabulator-separated txt-files. Because of the individual filenames all exported files can be stored in the same directory. An example of a filename for an exported file is: Result list – 021030 XLS.txt The message box, which appears when files are exported, shows the location and name of the exported file, see figure 28. 6.
6 Utilities tab The viability report can be printed (using the default print er) or exported by clicking the “Print” or the “Export” button. All of the saved results are printed or exported when the buttons are activated, it is not, as for the result list, possible to choose which results are to be printed or exported. Once a viability report is exported a message box appears. The message box shows the location and name of the exported report, see figure 29.
6 Utilities tab C:\Nucloeview\Export data The file names of the viability reports are constructed in the same manner as the result lists. The first part is a prefix, Viability list -, the middle part is the date of the session from which the viability report is derived, YYMMDD. The last part is “XLS” to indicate that the file can be imported into e.g. MS Excel. The exported viability reports are tabulator separated txt files.
6 Utilities tab Figure 31 Open Excel 2. Locate the file to import in the directory: "C:\Nucleoview\Export data" and open it (doubleclick it or highlight it and click the “Open” button). If you cannot find the file in the directory ensure that you have selected “Text Files” in the "Files of type" field at the bottom of the dialogue. Once the txt-file has been opened the Text Import Wizard appears, see figure 32. Figure 32 Import to Excel step 1.
6 Utilities tab 3. Check that the radio button under “Original data type” is set to “Delimited”. If this is the case, click “Finish” to import the file. If the radio button is set to “Fixed width” change it to “De limited” (using the mouse). Click “Next” and a new dialogue will appear, see figure 33. Figure 33 Import to Excel step 2. 4. The delimiter must be set to “Tab” as shown in figure 33. This is normally the default setting for Excel. Click “Finish” to import the data into Excel. 5.
6 Utilities tab Figure 34 Data imported to Excel 6.4.1 Set decimal symbol To import reports to Excel ensure that the decimal sym bol used by Windows is set to "." (period) and not "," (comma). To check that the decimal point is correct or to change it, follow the directions below. 1. Open “Control Panel” through the Windows Start menu. 2. Select the "Region and Language" options. 3.
6 Utilities tab Figure 35 Setting decimal symbol using the Region and Language o ptions in Windows Control panel. Only part of the dialogue is shown. 4. Check if the Decimal symbol is “.” (period), see figure 35. If the Decimal symbol is “,” (comma) change it to “.” (period). The decimal symbol has now been set and import of files into e.g. Excel can start. Please note that changing the Region and Language options affects other programs. 6.
6 Utilities tab Figure 36 Report header information. Changes made to the report header will affect the result lists, exported data and the viability reports. A viability report will only show the changed report header if it was changed before the first viability calculation of that particular report was saved. 6.6 Default settings for NucleoView TM NucleoView offers the possibility to change the default settings used when data is transferred from a NucleoCounter.
6 Utilities tab Figure 37 Customized default settings for NucleoView. Next time the “Change settings” button is activated, the new default settings appear again. The old default settings will appear only if NucleoView has been closed down and launched again, this can be used as an easy method to change the settings back to the factory set default values (by clicking “Save settings”). If the “Change settings” button has been activated but no changes are to be made, click “Change settings” again.
6 Utilities tab Figure 38 This message box is displayed when no text editor is configured and the Utilities tab is activated. 2. Activate the "Configure"-button below "Text Editor" in the Utilities tab. 3. Click OK when the message box shown in figure 39 appears. Figure 39 When this message box is displayed click OK and locate the WordPad application. 4. The dialogue shown in figure 40 appears. Locate “wordpad.exe”, highlight it (using the mouse) and click Open.
6 Utilities tab Figure 40 This dialogue appears when WordPad or Notepad is configured as text editor. 5. The message box shown in figure 41 appears when WordPad or Notepad has successfully been configured as text editor. Click OK and proceed to define the font for the text editor. Figure 41 This message box indicates that a text editor has been successfully configured. 6.7.1 Define font for WordPad To create reports with results in columns the font for the text editor must be defined.
6 Utilities tab 1. Open WordPad and select “Save as” from the File menu. The dialogue shown in figure 42 appears. 2. Choose the location to save the file to be the Nucleoview folder (usually C:\Nucleoview). 3. In the bottom of the dialogue change the “Save as type:” to “Text Document”. Make sure there is a checkmark in the check box to the left of “Save in this format by default”. If there is no checkmark present set it using the mouse. 4. Change the file name to “Document.txt”. 5. Click “Save”.
6 Utilities tab Figure 43 Confirm the setup for WordPad by clicking “Yes”. 7. 6.7.2 Exit WordPad. Define font for Notepad Similarly Notepad can be set up for NucleoView, follow the directions below. 1. Open Notepad. 2. Choose “Font…” through the Format menu. The dialogue is shown in figure 44.
6 Utilities tab Figure 44 Defining the font for Notepad. 3. Choose the font Courier, Font style Regular and Size 10 as in figure 44. Now Click OK and exit Notepad. Notepad will use the font Courier, size 10 regular.
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7 Troubleshooting 7 Troubleshooting Occasionally difficulties with the NucleoView software may occur. In the following a short description and suggested action is given. 7.1 Quality of the sample Through the CM file image it is possible visually to assess the quality of the sample preparation and thereby the reliability of the measurement by looking at the “star ry sky”. The measurement is reliable if the stars or white dots are distributed separately and evenly over the image.
7 Troubleshooting Figure 46 Not connected Figure 47 Connected If "Not connected" is the status then check the USB cable. When the NucleoCounter is turned off this status will also be the case. If data still is not received quit NucleoView and close the NC Receiver. Then open NucleoView and check that the NC Receiver is also started. If necessary, restart the computer before opening NucleoView again.
7 Troubleshooting The following procedure shows this. 7.2.1 Test Image transfer from the NucleoCounter. Press <5> <1> on the keyboard of the NucleoCounter. Press enter < >.
7 Troubleshooting The Test Image is present, a “saw-tooth” pattern is shown in the Object Intensity Histogram and if the “Test Image OK” indicator is visible (and green) the image data transfer from the NucleoCounter to NucleoView is working. 7.3 NucleoView “freezes” If NucleoView ”freezes” or does not respond, quit the program using the “QUIT” -button in the Measurement tab. Close down the NC Receiver. Then restart NucleoView and the program should be ready for use again.
7 Troubleshooting Figure 48 Windows Task Manager – Performance when running NucleoView Figure 48 shows the Windows Task Manager. During normal operation of NucleoView the CPU usage will typically be less than 20% however it can peak to 90%, when a new file is received or when another file from the file list is selected.
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8 Technical specifications 8 Technical specifications 8.1 NucleoView™ software System requirements For operating systems see table 1 below. 14 15 USB 1.1 port . Display Screen Area: Minimum 1024 x 768 . Table 1 Functionality of NucleoView and the USB driver on computers running different operating systems.
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9 Appendix 1: Printed result list 9 Appendix 1: Printed result list Below is an example of what the result list looks like when it is printed. On top of the page is a header and below are the chosen results from the active session including comment and operator. c:\nucleoview\data files\021218\Result list - 021218 PRN.txt Company Address1, Address2 Department NucleoCounter S/N: 002-09 Printdate: 18. december 2002 Printtime: 10:45 File name Cells/ml (cass.) MF 021218-001.CM 6.5 x 10E4 1.
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10 Appendix 2: Printed viability report 10 Appendix 2: Printed viability report Below is an example of a printed viability report. On top of the page i s a header and below that are the files, results of the analyses and the calculated viability in cells pr. mL and %. C:\Nucleoview\data files\021218\Viability list - 021218PRN.txt Company Address1, Address2 Department NucleoCounter S/N: 002-09 Creation date: 18. december 2002 Creation time: 08:45 Total cell count File name Cells/ml (cass.) MF 021218-002.
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11 Appendix 3: Default settings for Yeast samples 11 Appendix 3: Default settings for Yeast samples The settings below are suggested default settings for users with very high cell count. This can be the case when Yeast fermentation samples are being analyzed using th e NucleoCounter YC-100 instrument. Figure 49 Suggested settings for very high cell counts in e.g. Beer or Wine Yeast fermentation samples using the NucleoCounter YC -100.
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12 Index 12 Index Adding comment ................................. 18 Adding operator .................................. 18 Import data into Excel ......................... 36 Installation procedures ......................... 1 Intended use ......................................... v Browse button .................................... 19 Browse files from active session .......... 19 Browse stored files.............................. 19 Calculate viability ................................
12 Index Names of exported files ................... 33 Large objects in the image ............... 49 Print ................................................ 31 NucleoView “freezes” ...................... 52 Returning to active session .................. 20 Utilities tab ......................................... 31 Save image .......................................... 23 Save image button ........................... 24 Save viability calculation .....................
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Ver. 2.3 3-August-2012, 991-0006. The information contained herein is to the best of our knowledge accurate and complete. However cell species and cell environments may vary in property. Therefore systematic and/or random deviation between estimates obtained by the Nucle oCounter™ and other cell counting methods may occur. As such, nothing contained or stated herein including results obtained from use of the NucleoCounter™ or NucleoCassette™ shall be construed to imply any warranty or guarantee.
