From Windows click on the 'Start' menu, move the cursor to select Programs/PerkinElmer Software and move the cursor to select PixCel.
The following is some of the terminology used in this manual and is designed to help you get the best from your software.
NOTE : Important tips or notes for special attention when using the software.
WARNING!!! : Attention should be paid to the information contained here. Information regarding misuse or carelessness is advised.
Keyboard combinations : A plus sign (+) used between key names indicates those keys must be pressed at the same time. For example 'Press Alt+F' means you press both the 'Alt' key and the 'F' key at the same time.
Using the mouse : 'click' - press and release the left mouse button, 'double click' - press and release button twice in quick succession, 'click and drag' - press button, hold whilst moving the mouse, then release.
Menu commands : These are referred to in the form Menu name/Menu command. For example 'Select File/New' this can either be executed by: Using the mouse to select first the 'File' menu and then the 'New' function from the menu, or Pressing the 'Alt' key and the underlined character in the name at the same time. ie: Alt+F, followed by n.
After starting the software the a window appears on your screen looking like this.
NOTE: The Software toolbar is a flexible dockable toolbar. It can be picked up and moved left, right, top or bottom, docked or left floating for your convenience. The Camera control tabs and View & navigation toolbar are also left or right dockable or can be floating. This window can be maximized (using the standard Windows functions, found in the top right hand corner of the screen) by clicking on the 'underline' in the top right hand corner of the menu to reduce application to the Windows bottom menu bar; click on the double screen to allow greater detail of the image to be observed, or click on the X to exit the application and return to the main Windows screen.
The Main menu bar is located at the top left hand side of the screen. This is a static menu bar incorporating the standard Windows functions. The menu comprises a range of facilities which when clicked activates a 'pull down' list of further options. See Controls reference for a more detailed account of each facility. A tick mark where appropriate, indicates the option is initialised.
File Click on File or use Alt+f to access: New, Open, Save, Save As, Import, Export, Configure, Print, Print Preview, Print Setup, Recent files and Exit.
Edit Click on Edit or use Alt+e to access: Undo, Cut, Copy, Paste, Delete and Select all.
View Click on View or use Alt+v to access: Toolbars, Status bar, Mapping, Autoscale Prefs, Statistics, Lookup tables , Image, Plot, Histogram, Pixel values, User values, Rectangular Selection, Sequence images, Black Level Image and Flatfield image.
Acquire Click on Acquire or use Alt+q to access: Live Grab, Sequence Grab, Black Reference, Flat Field Reference.
Analyse Click on Analyse or use Alt+a to access: Image analysis, Dark subtraction and Shade correction.
Hardware Click on Hardware or use Alt+w to access: Status, Initialise, Reoptimise.
Help Click on Help or use Alt+H to access: About PixCel..., Contents , System Info...
The Toolbar is located along the top left hand side of the screen. This is a dockable toolbar allowing it to be moved left, right, top or bottom, docked or left floating. It can also be 'switched off' and removed from the screen by accessing View/Toolbars.. option in the main menu. The toolbar comprises of a range of icons which are explained below in detail from left to right:
New file Select the New file icon to clear the image area to start a new image. Alternatively select from the main menu File/New or Ctrl+N.
Open file Select the Open file icon to open an existing image file held on disk. Alternatively select from the main menu File/Open or Ctrl+O.
When the Open dialogue box appears, select the image from the File name list and choose the OK button. If the image is not listed, then a search of the folders can be actioned by selecting the appropriate directory, file type and/or file name. Either double click the item or highlight the option and click the Open button to select.
NOTE: only a .apf or .opf files or Imager 1, 2 or GCI files which have been saved using the ‘Save file’ option can be opened with this method. All other files can be opened by using the Import facility.
Save file To Save an image in the software internal file format, select the Save file icon. Alternatively select from the main menu File/Save or Ctrl+S.
If saving for the first time, the Save As dialogue box, will appear allowing the user to select a directory in which to save the file, type a file name, and select a file type. Within a sequence the images can be saved as 'All' for the sequence as a whole, 'Current frame' for the image currently in view on the screen, or a particular frame or frames within a sequence. Select and check against the corresponding requirement and enter the frame numbers if appropriate. If the image has been previously saved, all new changes will automatically be saved to the original file name and location, and the original file data will be overwritten.
NOTE: The saved file is in ‘PixCel’ format i.e. .apf or .opf, which contains additional information about how the image was collected.
Cut The Cut feature is functional only when using the Object Linking and Embedding (OLE) feature. (Advanced future applications only)
Copy The Copy feature allows the image view or a 'rectangular' selection to be copied and placed on the Windows clipboard for retrieval by another package ie: Word, Excel, Paintshop Pro etc. To create a 'rectangular' selection, click in the image view with the left hand mouse button, depress the Control keyboard button simultaneously and drag a 'rectangular' area. Select the Copy icon to copy the selected area or image and to paste it onto the clipboard. Alternatively select from the main menu Edit/Copy or Ctrl+C.
Paste Select the Paste icon to paste the selected area from the clipboard to the area or into a document or image of your choice. Alternatively select from the main menu Edit/Paste or Ctrl+V.
Toolbars Select the Toolbars icon to access the Toolbar configuration dialogue box.
By individually clicking in the check boxes to select the Main, Camera, View, Camera Init/Optimise and Acquisition Controls will enable or disable the display of the toolbars and control boxes on the screen. Click on OK to accept changes, Cancel to abandon changes made or the X button in the top right hand corner of the dialogue box to close the toolbar dialogue box and return to the main image window. Default settings are Main Controls, Camera Controls and View Controls. To re-view the toolbars, select View from the main menu, select Toolbars.. and re-select the options available.
Mapping (Brightness/Contrast) The mapping function controls the display look up tables to adjust brightness and contrast. Select the Mapping icon to access the Image mapping dialogue box. Alternatively select from the main menu View/Mapping.
By selecting the centre button or the arrow buttons either end of the slide scale indicator, the brightness or contrast levels can be adjusted between the low and high thresholds. Minimum and maximum levels are indicated at the extremes of the slide scale bar. Alternatively, on either side of the brightness/contrast image, the dotted line can be picked up and dragged to set the low and high values accordingly. This in turn changes the values in the low and high boxes together with moving the sliding scale.
If particular values are required, these can be directly typed into the low and high boxes. Any changes made can be applied by selecting the Apply button. The Reset button will cancel any changes made and revert to the original image values, i.e. the values that appeared before moving the sliders or dotted line.
The Autoscale function can be customised to allow closer autoscale data match to that of the image being captured. Refer to Chapter 4 View/Autoscale Prefs....
This function is only available when the Image view is selected.
WARNING!!! PixCel is a multi-tasking Windows program. The mapping functions are used by the data capture procedures. If you also use the mapping functions during data acquisition, serious confusion can occur. The best strategy is to only adjust mapping once data taking has completed.
Autoscale Preferences: The Autoscale function can be customised, to allow closer autoscale data match to that of the image being captured. Autoscale initiates the automatic selection of a number of high and low pixel grey values and adjusts the settings according to the values found.
Click on Autoscale Prefs. to view the Autoscale Model dialogue box. Select the option required by clicking the appropriate radio button. Further adjustment can be made by placing the cursor on the dotted lines either side of the histogram indicated within the dialogue box. Click the Apply button to accept changes or Close to abandon changes and revert to the main window.
Statistics Select the Statistics icon to access the Statistics information box. Alternatively select from the main menu View/Statistics.
The statistics information box indicates values appropriate to the region of the image area selected, even when the region box is not visible. These include measurement on the data contained in the area of interest as well as the description of the area selected (size, position and area, in number of pixels). The calculated data values include: Maximum, Area, Minimum, Std dev, Skew, Kurtosis, Median, Upper quartile, Mode, Lower quartile, Mean, % Even. This is a non editable feature, although it can be copied to the clipboard using Ctrl+C.
NOTE: the region used by the statistics box is independent of the visible screen zoom and may be shown by pressing the 'rectangle selection' icon even if the region box is not visible.
Rectangle selection The current rectangle selection is the area indicated by clicking this icon or by holding the shift key down, clicking and dragging with the left hand mouse button between two points with the Image view window. The box created is the rectangle selection. It may also be changed by entering relevant details within the Properties dialogue box. Click on the Rectangle selection icon to enable or disable the display of the rectangle selection.
Line selection The Line selection is a straight line on the image, indicated by clicking the left hand mouse button and dragging between two specific points with the Image view window. It may also be changed by entering relevant details within the Properties dialogue box. Click on the Line selection icon to enable or disable the display of the line selection.
Print Select the Print icon to access the Print dialogue box. Alternatively select from the main menu File/ Print or Ctrl+P. The standard Windows 95 printer dialogue box will appear which will allow the user to indicate which printer to use, which pages to print, and how many copies. Selecting the Properties button within the Print dialogue box will allow the further selection of the size and orientation of the paper, resolution and intensity of graphics, choice of fonts and device quality options. Select OK to accept changes or Cancel to abandon and return to the image window.
About Select the About icon for access to the HTML pages containing information about the PixCel software.
Live Grab Select the Live Grab button to take an image with settings as indicated on the Camera control tab. Images are taken and displayed continuously until the Stop button is pressed.
Sequence Grab Select the Sequence Grab button to take a sequence of images as previously set in the Sequence control tab and the Camera control tab.
Twain Transfer See Appendix B for full a explanation.
The Camera or Sequence control tabs contain information regarding the camera settings. Click on the tab to view the option required. The Camera control toolbar is a dockable toolbar allowing movement to left or right of the image window, or can be left floating. The Camera control toolbars can be 'switched off' and removed from the screen by selecting View/toolbars.... The toolbar configuration box allows selection of which toolbars are visible or disabled.
The View and navigation toolbar is located at the bottom of the screen. It is a dockable toolbar which can be moved left or right, left floating, or can be 'switched off' and removed from the screen by using the View/Toolbars... option. The toolbar comprises a range of icons which are explained below in detail from left to right.
Image Click on the Image icon to display the image in the main window.
Plot Click on the Plot icon to view a line graph of the values under the current line selection.
Histogram Click on the Histogram icon to view the grey level values under the current rectangle selection as a histogram.
Pixel Values Click on the Pixel Values icon to show the grey level values of the current rectangle selection in a spreadsheet format.
User values Click on the User values icon to view the current control parameters.
First Frame Click on the First Frame icon to go to the first frame in a sequence.
Previous Frame Click on the Previous Frame icon to go to the previous frame in a sequence.
Frame # The Frame # box indicates the number of frames in a sequence and the number of the frame being viewed at the time e.g. Frame # 1 of 2 indicates you are viewing image one in a sequence of two. To view a particular image enter the image number in the Frame # box and press the enter key.
Start Playback Click on the Start Playback icon to start the review of all the images in a sequence. Playback stops when the last frame has been viewed unless toggle looping has been enabled.
Stop Playback Click on the Stop Playback icon to stop the review.
Toggle looping Toggle looping is a review mode that starts at the first image again when the last has been reached etc. Click on the Toggle looping icon to select the looping of image sequences.
Next Frame Click on the Next Frame icon to view the next frame in a sequence.
Last Frame Click on the Last Frame icon to view the last frame in a sequence.
Playback speed Click on the Playback speed icon to access the Set Playback Speed dialogue box.
Use the slide controls to vary the sequence playback speed and click Apply to apply the changes and Close to close the dialogue box and return to the main image window.
The Status bar is located to the bottom of the screen. It is a static toolbar and cannot be moved within the screen although it can be switched off from the View main menu. The left side provides information about the state of the program. The boxes left to right provide information on the camera acquisition status together with cursor position information. It comprises a number of areas that are explained below in detail from left to right.
Camera Status Indicates the mode in which the camera is operating e.g. Ready to grab an image, Re-optimise for optimisation, or Waiting when waiting for a trigger.
Pixel Grey level of pixel under the cursor.
X position Y position X and Y position of the image pixel location of the cursor on the image.
Frame time Shows the time from the start of acquisition of each frame in a sequence.
Base Electronics base pixel value, typically 200-1000 and is updated periodically.
Sd (Standard Deviation) Current readout noise in data numbers of the system and is updated periodically.
CCD CCD operating temperature (disabled with UltraPix) is indicated in this box, in degrees C.
Sink Heat sink temperature (disabled with UltraPix) is indicated in this box, in degrees C.
Using the View and navigation toolbar the following different types of view are available:
By placing the cursor over the icons displayed in this toolbar the description will be shown in the status bar information box located at the bottom left hand side of the screen. To use the function click on the icon. Alternatively, for Plot, Histogram, Pixel and User values, click on View to make your selection or use the Alt+V keys and select.
Image view
The image view is the main image display window. Within this display window the images in the captured sequence can be viewed. The image is viewed by clicking the image icon on the view and navigation toolbar or View/Image view from the main menu.
If the image displayed is larger than the window, use the window scrollbars located on the right hand and lower side of the main window to see the rest of the image.
The Status bar shows the current cursor position and pixel intensity when the cursor is moved within the image.
To view an area of interest, press and hold the shift key then drag the mouse with the left button pressed to draw a rectangle around the desired area (zoom in). This is used to make the 'rectangular' selection required, and then the image is re-displayed so that the selection now fills the available viewing area. Use the mouse with the Ctrl key to select an area that the current view should fit into (zoom out). This is used to make a new 'rectangular' selection and the image display is updated accordingly. To revert to the original full image, click the right hand mouse button to activate the zoom in/out box. Select x1 to revert back to the original sized image or choose another option from the list shown. A wide range of zoom factors are available.
Clicking on View/ Statistics in the main menu, or the statistics icon on the software toolbar, will bring the statistics dialogue box into view. This will give statistical information for pixels in the current rectangle selection.
NOTE: Should you want to get statistical data on a small region of the image this region may be selected as above. Using the right mouse button to zoom in or out to view another part of the image leaves the region selected for statistical analysis unchanged, until another rectangular selection is made as above. Click on the X button to close the statistics dialogue box and return to the image window.
Within the image view, press the left hand mouse button and drag to produce a line which tracks the mouse. When the mouse is released the position of the ends of the line will define the 'line' selection and the line is removed from the display. The co-ordinates of the line are used for the plot view.
By clicking the right hand mouse button, an option box will allow access to: Zooming in and out, Properties, Copy to the clipboard, Print and Export.
Zooming in/out is accessed by clicking in the image area with the right hand mouse button. Move the mouse to place the cursor on the chosen option e.g. 1:1, etc and size to fit. Clicking on the chosen option will change the image and close the zoom in/out option box. To close the zoom in/out option box without selecting an option, click within the image window again.
Properties can be viewed, in image view only, by clicking with the right hand mouse button in the image area and clicking on properties. The properties dialogue box provides information on the sequence title, when the image was created and the image size details. The line selection and rectangular selection are accessible for checking or changing. Tick boxes allow vertical or horizontal line selections to be made. Data may be typed as required.
Select View/Mapping from the main menu or use the mapping icon on the software toolbar to adjust contrast and brightness. Click on the X button to close the mapping dialogue box and return to the image window.
NOTE: the autoscale check box can be customised to give a better result with certain image types. Refer to Chapter 4 View/Autoscale prefs...
Lookup tables (LUT) can be selected from the View menu. A choice of Grey scale, Pseudo colour, Red ramp, Green ramp, Blue ramp, Invert, Equalise, Logarithmic or Square root, can all be made by moving the cursor to the required option and clicking. A tick mark indicates which lookup table is in use.
Use the First/Last/Next/Previous/Frame #/Play and Stop buttons on the view & navigation toolbar to move from one image to another in the sequence.
Use the Edit/Copy option from the main menu, Ctrl+C, or the copy icon to copy the 'rectangular' selection to the clipboard. The image can be pasted (Edit, Paste or Paste Special) into another application e.g. Word, Excel or another package. The copy function is also available by clicking with the right hand mouse button in the image window and choosing copy from the zoom in/out option box. When the copy option is clicked the image is transferred to the clipboard.
Select File/Print from the main menu, Ctrl+P, or the print icon to print the whole image. The image can be previewed before printing by using the Print Preview menu option. The page can also be changed from landscape to portrait, letter to A4 etc. using the page setup option from the same menu. The print function is also available by clicking with the right hand mouse button in the image window and choosing print from the zoom in/out option box. At this point the print dialogue box will appear.
Plot view
A pixel plot is a graphical representation of the grey level (pixel intensity) against the pixels of the Line selection. Data from the Pixel values can be cut and pasted into most Windows compliant software for further analysis and display.
To display a Plot of the image, select the plot icon. The icon will activate and appear depressed. Alternatively, click on View/Plot from the main menu. The main window will show a line graph with values corresponding to the grey level pixel fluctuation along the current line selection (see Using the Software Toolbar). Place the cursor on the plot line and the corresponding value will be displayed. To revert to the selected image click on the Image icon.
Use Edit/Copy, Ctrl+C, or click on the copy icon, to copy the graphical plot and values that make up the plot to the clipboard as a CSV (Comma Separated Value) and as a picture. This can be pasted (Edit/Paste Special) into Excel, Word or another package for further analysis.
Use the First/Last/Next/Previous/Frame # controls on the view and navigation toolbar to move from one image to another in the sequence. The plot is updated with the pixels from the new image under the line selection.
Select File/Print from the main menu, or Ctrl+P, or the print icon to print the whole plot. The plot can be previewed before printing by using the Print Preview menu option. The page can also be changed from landscape to portrait, letter to A4 etc. using the Page Setup option from the same menu. The print function is also available by clicking with the right hand mouse button in the image window and choosing print from the zoom in/out option box. At this point the print dialogue box will appear.
Data from a plot can be dragged from PixCel into a Microsoft Excel spreadsheet. Start both PixCel and Excel. Arrange the PixCel and Excel windows beside one another. Load a sequence into PixCel, select the plot view and press and hold the left mouse button in PixCel. Move the cursor to the Excel window and release the cursor. The data has now been copied across. This saves time compared with using PixCel's Edit/Copy and Excel's Edit/Paste special controls.
Plot is also very useful for focusing. Draw a line across an element within the image that should have sharp contrast (sharp transition when in focus), select plot mode, then use live grab. The best focus is typically when the plot has the steepest transition in the plot mode.
Mapping controls are not available in this view.
Histogram view
A histogram is a graphical representation of the frequency of occurrence of each grey level (pixel intensity) within the rectangle selection. It can be calculated on the whole or just part of the image. Data from the histogram can be cut and pasted into most Windows compliant software, for further analysis and display.
To display a Histogram of the image, select the histogram icon. The icon will activate and appear depressed. Alternatively, click on View/Histogram from the main menu. The main window will show a bar graph histogram of the current rectangle selection (see Using the Software Toolbar). Place the cursor within the histogram and the corresponding value will be displayed. To revert to the selected image click on the Image icon.
Use the First/Last/Next/Previous/Frame # controls on the view and navigation toolbar to move from one image to another in the sequence. The histogram is updated with the data from the new image under the rectangle selection.
Click the right hand mouse button and an option box will appear allowing the selection of either a bar or line histogram. A tick mark indicates the option currently chosen.
Use Edit/Copy, Ctrl+C, or click on the copy icon, to copy the graphical plot and values that make up the plot to the clipboard as a CSV (Comma Separated Value) and as a picture. This can be pasted (Edit/Paste Special) into Excel, Word or another package for further analysis. The values pasted in the output have as the first two numbers the grey level of the first bin of the histogram and the quantisation factor (the number of consecutive data numbers that are used to make a single point in the histogram).
Select File/Print from the main menu, Ctrl+P, or the print icon to print the histogram. The histogram can be previewed before printing by using the Print Preview menu option. The page can also be changed from landscape to portrait, Letter to A4 etc. using the Page Setup option from the same menu.
Data from a plot can be dragged from PixCel into a Microsoft Excel spreadsheet. Start both PixCel and Excel. Arrange the PixCel and Excel windows beside one another. Load a sequence into PixCel, select the histogram view and press and hold the left mouse button in PixCel. Move the cursor to the Excel window and release the cursor. The data has now been copied across. This saves time compared with using PixCel's Edit/Copy and Excel's Edit/Paste special controls.
Mapping is not available in this view.
Pixel values view
Pixel values is a 'spreadsheet' type representation of the data in the image. It shows the pixel values at each X and Y location. Data from the pixel values can be cut and pasted into most Windows compliant software for further analysis and display.
To display the pixel values of the image, select the pixel value icon. The icon will activate and appear depressed. Alternatively, View/Pixel value from the main menu. The main window will show a spreadsheet of the current rectangle selection (see Using the Software toolbar). The extreme pixel values of the image are highlighted in the table as red for the maximum and blue for the minimum values. To revert to the selected image click on the image icon.
Use the First/Last/Next/Previous/Frame # controls on the view and navigation toolbar to move from one image to another in the sequence. The spreadsheet is updated with the data from the new image under the rectangle selection.
Use Edit/Copy, Ctrl+C, or click on the copy icon, to copy the spreadsheet as a CSV (Comma Separated Value). This can be pasted (Edit/Paste Special) into Excel, Word or another package for further analysis.
Select File/Print from the main menu, Ctrl+P, or the print icon to print the spreadsheet. The spreadsheet can be previewed before printing by using the Print Preview menu option. The page can also be changed from landscape to portrait, Letter to A4 etc. using the Page Setup option from the same menu.
NOTE: only the pixels in view are printed. It is advisable to select the area of specific interest before copying or printing, as the amount of information in a full screen grab being copied to the clipboard will cause an extended delay in copying or printing. Also avoid selecting much larger areas than you need. Programs such as Excel do not handle large data sets efficiently.
Data from a spreadsheet can be dragged from PixCel into a Microsoft Excel spreadsheet. Start both PixCel and Excel. Arrange the PixCel and Excel windows beside one another. Load a sequence into PixCel, select the pixel values view and press and hold the left mouse button in PixCel. Move the cursor to the Excel window and release the cursor. The data has now been copied across. This saves time compared with using PixCel's Edit/Copy and Excel's Edit/Paste special controls.
User values view
User values are the parameters used to acquire the image or sequence of images and includes the camera control monitored voltages. This is a non-editable feature.
To display the User values, click on the user values icon. The button will appear depressed. Alternatively, select View/User values from the main menu. Use the window scrollbars located on the right hand side and bottom of the main window to pan and scroll.
The editable values that were used when a sequence was captured are also displayed. They include all the camera, sequence and focusing parameters as well as the state of the electronics.
