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Frequently Asked Questions

What does the Mode Button do? The mode button affects how the images are loaded, operated on and saved. Images can be tiled, scrolled, and zoomed together.
Single mode - Works on the FRONT image window. Click on the window you wish to use.
Select mode - Presents a dialog in which you select the windows on which to work.
Group mode - Works on the FRONT image window and all others in its group.
All mode - Works on all image windows.
How does the mode button affect the XY scatter plots? The mode button does not affect making the plots, but once the plot is made, it is affected in the same way other images are affected (tiling, zooming, etc.).
How do you pick which group does its thing? The group with the FRONT image window is the selected group. The layer (depth) of other windows does not matter. Just click on one of the windows in the group.
How do I use the traceback tool?
Make sure the XY scatter plot is visible.
Click on the Traceback button.
Draw a line on the XY plot. This is the fixed side of a parallelogram.
Draw another line roughly perpendicular to the first line - this is an adjacent side of the parallelogram, which will be moveable while you hold the mouse button down.
How do I find the centroid of an image or a spot in an image?
'Info -> Rect stats' gives an intensity weighted centroid ('C Mass', pixel units for images. I'm working on something better for XY scatter plots).
Set the rectangle first. For the whole image, use 'Rectangle -> Select all'.
Which images are reported depends on the mode button.
How do I select a rectangle? (Select using one image. Can affect any image.)
Make sure the image you want to use is visible. (at least a part of it anyway).
'Rectangle -> Draw'
Immediately draw the diagonal of the rectangle on the image.
This will set the Image Rectangle parameter, or change it if it was set already.
The rectangle disappeared. How do I get it back? 'Rectangle -> Show'. The rectangle is stored as a parameter in 'Info -> List Parameters', 'Image Rectangle', as x1 y1 x2 y2, upper left corner to lower right corner. (the origin of the images is at the upper left). The rectangle is drawn temporarily, and will disapear whenever the window is redrawn.
Conversely, When I draw a new rectangle, the old one doesn't go away. How do I get rid of it? Redraw the window with 'Arrange -> redraw', then 'Rectangle -> show' to display the new rectangle again.
Why two Info buttons? The Info button at the lower left concerns Lispix in general - location of data, memory usage, control parameters, help. The Info button in the center concerns image windows - sizes, limits, properties.
Why doesn't 'Info -> Pixel info on click' do anything?
* If the text window doesn't show up when you click on an image, let me know.
* If you are asked to select windows after each click, use another image mode.
* If you see the text window, it might need scrolling to the bottom to see the results.
When I zoom an image, it turns all white! What happened? The image is scrolled out of the window. Use 'Arrange -> Size to image' to bring it back. [If this makes the window too big, leg me know and I'll add a 'Center in window', or 'Reset' or something to bring the scroll position to something sensible.] The image zooms about the center of the window. Small images, such as the xray maps, are shown at the upper left of a window that is too large, thus the image gets zoomed out of the window. If the windows are sized to the image before zooming, they should not appear enbtirely white after zooming.
How do I get rid of those small titles in the image windows? 'Arrange -> Small titles off'
How do I print images? Lispix does not print directly. I print using Photoshop, after transferring the image using a screen grab or writing a TIFF file. The screen grab is necessary to print graphics, labels, axes, etc.
How do I save plots or images with graphics, labels, axes etc.? Use a screen grab. Lispix saves only image data and the look up table.
Why are some of the menu items grayed out or disabled? These items are in MacLispix and have not been put into Lispix, simply because I haven't needed them yet. If you need them, let me know and I'll try and put them in right away.
The image flickers like mad when I use a threshold or contrast slider. This happens on the PC when the image does not completely fill the window. Make sure the image is not scrolled out of bounds (even a little bit), or use 'Arrange -> Size to image'.
What is a mask? A mask is a binary (bit) or black/white image. White pixels are considered 'on', or 'foreground', or 'object'. Black pixels are background. Masks can be used to control various statistical operations, and the traceback.
Masks are made using the 'Mask' button. 'from Rectangle' and 'from Threshold' use the mode button and the rectangle or thresholds that are already there. 'Mouse parallelogram' works on the front image - mouse a parallelogram on the front image and see the mask.
How do I draw a parallelogram? Draw a line. This line is fixed. (Let mouse button up.) Draw another line approximately perpendicular to the first. The resulting three sides to the parallelogram are movable until you let up on the mouse.
Why doesn't a window revert to gray scale when I close a slider? Change the setting with 'Color -> gray on close?' Otherwise, use the 'Gray Scale' button.
How can I get the slider to go away when the image is closed? 'Arrange -> Close' in Group mode, with the image in front.
I get sliders and images mixed up. How can I tell which goes with which?
The title for the slider includes the title for the image.
The slider and image are in the same group. Click on one of them, change the mode to 'Group Mode', and then use 'Arrange -> Pop to front' to see them both.
Use 'Group -> List members' to see who goes with whom.
How do I find out the range of pixel values of a group of images? Select the desired mode. 'Scale -> fixed limits' will default to the global range of data. If performed, this operation scales all of the images to the given limits. Alternatively, 'Info -> Sizes & Limits' will list the range for each image individually.
How do I change the background color of a scatter diagram? Any color of a pseudo-colored image can be changed with 'Color -> change one color'. Since the scatter diagrams made with the 2&3Variable widget are images (scatter diagrams of all the pixels in an image), rather than plots, and since they are false colored (that is what the slider does that appears with the window), use 'Pick color', then 'Color -> change one color', and pick 0 for the level.
Will Lispix ever have an 'undo' command? No. If there is a particular situation that is often annoying, let me know - perhaps I can improve the user interface there.
Function has no help message. Please let me know and i'll add it.
The 'Group -> List members' doesn't list all of my windows. It works according to the mode button. Change the mode button to 'all im mode' to make sure all of the windows are listed. (If they are ALL in the same group, the group mode will also work, but then you haven't learned much. :8o).
I have trouble loading images in the select mode. Make sure that ONLY the proper images are selected. Note that the first file in the list is selected by default. If you hold down the control key while making multiple selections - watch out for that first file.
'File -> Open' doesn't do anything. -- The default read directory may no longer be there. Use 'File -> Show defaults', 'File -> Clear defaults', or 'File -> Set default read directory.'
My image files sometimes don't appear in the file selection dialog ('File -> Open'). In the 'Single' mode, you should see your images, and can select one of them. In the other modes, the dialog is to select a directory, and the images will not appear. After selecting the directory, a list of images appears for selection of one or more images at a time.
Image types and file extensions that Lispix recognizes in 'File -> Open', can be listed with 'File -> File Extensions'.
How do I load a tiff file that does not have a .tif or a .tiff extension. Lispix doesn't recognize it as a tiff file. -- Lispix recognizes files by their extension. The best was is to change the extension of the file. (If the TIFF file has no extension, Lispix will try to load it.)
There is a work around for tiff files:
Widgets -> Data Cube
Load -> as TIFF files
Image -> slices to windows
This works because the cube loader doesn't care about file extensions. The last step above is to make a separate window with the one tiff image, if you wish to do that and have loaded more than one tiff file into the cube.
Is there an easy way to change file extensions? 'Widgets -> Process Folder -> Change file names -> Change Extensions'.
How to I get conveniently to the HTML doc page for a particular button? If the button or command has a doc page, the name will follow the :html in the doc message that you see when you hold down the control key while selecting that button or command. After doing this, then click on 'Print this', then select and copy the HTML file name from LxDoc/... (to the right). Go to your web browser, which should already be at a Lispix doc page, for instance the Lx Doc home page. Then paste the page into the file (or url) name at LxDoc, and hit enter.
Where are some sample images? Sample images are in the 'Lx / Images' folder. You must download the images separately: I do not bundle them with the application archive because they double its size. The 'Demo' button has a few items that display sample images if they are there: 'Demo -> Betsy', 'Demo -> Display Koala', 'Demo -> RGB Koala'. Otherwise, use 'File -> Open' and navigate to 'Lx / Images / ...'
How do I get images from my microscope into my computer?
1) Directly - some microscopes save their images in files directly.
2) Use a frame grabber board. These boards often have drivers or plug-ins that work with
NIH Image or Adobe Photoshop. They go in your computer, and are wired directly to your microscope.
3) Scan prints or negatives. Lispix doesn't work with scanners, but NIH Image and Photoshop do.


How to I find or uncover a window that's under a bunch of others?


How do I make a montage or mosaic of images?
How do I make a scatter diagram using a mask? I want to do a plot using X ana Y pixels, ONLY where a mask pixel is white - ignoring pixels where the mask is black.
1) Get an X, Y and Z image. Threshold the Z image to make a mask.
a) 'Single' mode, click on Z image to bring to front.
b)Thresh -> Threshold Slider', select the thresholds you want.
c) 'Mask -> From Threshold'. Rename the threshold image if desired.
2)'Widgets -> 2 & 3 Variables'
a) Select the X, Y and mask images.
b) 'XY Scat -> 2D with mask.'
Does Lispix have key stroke equivalents for the buttons or menus? No.
Any easy ways to line up a fat profile plot perpendicular to a straight interface? Yes - turn the cursor on, position it near where you want the interface to be, then line it up on the interface using the adjustment points at the ends of the profile line.
How do I apply a gamma correction? 'Color -> Gamma slider'. If you want to save the corrected image, use 'File -> Save as TIFF'. {Note - 3/29/00 - this doesn't work yet, but should soon.} If you want to print the image, use a screen grab and print using NIH Image, Scion Image, ImageJ or the like. (Photoshop has its own gamma correction tool - see 'Image -> Adjust Levels' and slide the center triangle pointer.)
How do I 'do' the log 3-band color scale? This color scale is for use with K-Ratio maps and quantitated X-ray maps, where the concentration fraction (weight percent) ranges from 0.0 to 1.0. If you are doing something other than using the K-Ratio widget, first make sure the useful image pixel values range from 0.0 to 1.0 (outliers are ok). Then 'Widgets -> Kratio' if window is not already there, then use 'Color Scale -> log 3 band'.
How do I make the color scale itself? 'Edit -> Log Ramp', then 'Widgets -> K Ratio' if necessary, then 'Color Scale -> Log 3-band'. If the ramp width is greater than the height, it will be horizontal. The default is a vertical ramp.
Can I make the slice slider work for more than one cube image at a time? Yes. Sliders work on images in the same group.
Why does the Info window paste the last output in the middle of previous output, which I no longer care about? The result is confusing. -- Output is printed to the info window at the insertion point. Ways to avoid this mixup of output:
1) Close the info window each time. Lispix will make a new one.
2) Never click on the info window. If you do, click at the end to put the insertion point there.
3) Bug me to fix this problem. :8o).
When I tile images, Why dont' they mov?. - Make sure the mode button is set correctly - usually Group or All. Why don't I see all the images? They might be covered by other windows. Tiling the images does not bring them to the front. Use 'Arrange -> Pop to front' to do that.
How do I close all those extra images I no longer need without closing everything else?
1) Method 1
  • All image mode
  • 'Arrange -> Tile'
  • manually close the images you don't want.
2) Method 2
  • Select mode
  • 'Arrange -> Close', and select the images by title.
How do I scale an image when Lispix says it needs a pix image to scale? Lispix does not scale 8 bit images generally - the contrast slider ('Color sliders -> Contrast') or thermal slider are for that. Sometimes, however, scaling is needed that the sliders do not provide, such as histogram equalization ('Scale -> Equalize'). In that case, convert the image to a pix image with 'Adjust -> Byte to Pix', and then scale.