Results File

Mass measurements for an image are saved in c:\PCMass27\MassMeas\nkxxxxyy.smm when the image is closed (next image read or program terminated). This file can be opened with Notepad (the Windows accessory) or any text editor. Be sure to choose a font without proportional spacing to keep the columns straight. To import this into SigmaPlot or other plotting package, copy the .smm to a second file and trim off the extra descriptive information. When an image is read into PCMass, the program checks for a corresponding c:\PCMass27\MassMeas\nkxxxxyy.smm file and reads it into the results buffer. All subsequent measurements are appended to the same file. If you instead want to start fresh, use the "Erase_smm" option in the "File" menu. This erases the previous *.smm file as well as all the previous measurements. To delete the entries individually from the present session, starting with the most recent, strike the key.

Dispaly Results

Each stroke of the <i> key displays 40 entries from the current results file. If there are no more entries, the display resets to the first entry. You can also check individual particles by placing the mouse pointer close to the particle center. If a measurement has already been made on that particle with any model, it will be printed to the left of the present measurement, indicating the model # used, the sequential # and the values obtained. Note that this will obscure part of the profile display. The <o> key or "This File" option in the "Stats" pull-down menu provides an overview of what has been done on the current file. This starts with a display in the lower portion of the screen with one column for each of the lowest numbered 5 models used. Underneath the model # and name are nine entries consisting of mean, SD in %, number of measurements. There are three types of measurement: M for manual, T for trial and R for R-align (see description below of automated selection, 'T' and automated alignment, 'R'). Each type has three levels of testing: all particles of that type, only those passing the bkgRMS (brms) test for that model and those passing all tests for the model. Use the arrow keys to hi-light the measurement of interest. At the bottom of each column are compact histograms for each model with passing particles in green and failing in red. The right panel should show an expanded histogram for measurements in the highlighted category. Superimposed on the histogram is a Gaussian with the same mean and standard deviation.

View Particles by Bin

To see which particles are in various bins in the histogram, hold down the bar and position the mouse below the expanded histogram. All particles in the selected class will be marked in red on the original image (left panel) and those with mass values in the bin pointed to by the mouse will switch to white. Move the pointer back and forth under the peak to see where individual particles are highlighted.

Systematic Errors

Above the expanded histogram are scatter-grams for various image and fitting parameters. The purpose of this display is to highlight any systematic errors in mass measurement due to specimen imperfections or poor choice of selection parameters. The first horizontal row immediately above the expanded histogram compares (from left to right) Ml, Mm, X-coordinate, Y-coordinate and bkg plotted vertically versus Mp plotted horizontally. The individual measurement points are color coded as follows: GREEN = particles passing all tests, YELLOW = particles passing bkgRMS test but failing some other test and RED = particles failing bkgRMS. A straight line with a slope of 45 deg. indicates a high correlation between Mp and the particular parameter. The left panel, Ml (mass using local bkg.) versus Mp, should show nearly perfect correlation if the measurements were done correctly, with slightly higher errors in the Ml measurements, as discussed previously. The next panel to the right, Mm (Mass of fitted model) versus Mp should show a high correlation if the chosen model is a reasonable approximation to the particle of interest and the fitting is working correctly. The next three panels to the right should show no correlation between Mp and X position of the particle, Y position or background value. Any suggestion of systematic errors should be investigated, since averaging many particles will not remove such errors.

Validity of Measurements

Above the expanded histogram and the first scatter-grams is a second set showing correlation between Mp and the various parameters from the model fitting process: brms, rms, srms, size and height, with the selection "hurdles" and "cutoffs" indicated by dotted red lines. The dotted white line indicates a value of 1.0. In each case valid measurements should cluster and be well separated from measurements on problem particles and well above the respective "hurdles" and below the "cutoffs". The selection parameters can be changed by holding down the bar and dragging the appropriate line with the mouse pointer. (To see the effect on the histogram, strike the <o> key twice.) Selection parameters can also be changed permanently by editing the PCMmods.dat file and striking the <M> key (reload models) as described previously. Proper choice of model parameters should give both size and height scatter-grams centered vertically near 1.0 (dotted white line) in their respective windows. If this is not the case, you can try a different model or adjust parameters on the selected model as described below.

Clear, Save Screen

Clear the screen at any time by moving the mouse to go back to a normal screen. Restore the screen to remove all overlays by striking <0> (zero key). Save the screen to the clipboard using and paste into a PhotoShop document for printing. Strike to redisplay the image with particles/segments of the highlighted type marked. Hold down while pressing to print particle number and mass next to each particle.

Image-average Gallery

Strike <]> to image-average particles entered using the current model and passing all selection parameters for that model. LA and SA images of the selected particles before rotation are displayed in a gallery in the right image. The left image shows expanded images of: LA image, rotated, translated and averaged (top left), 0.9*SA image (bottom left), LA minus 0.9*SA (top right) and LA minus model (bottom right). To add to a previous average, use <}> instead of <]>.

Updated 4 Oct 2007	Security Notice   Webteam   Site Map   STEM   Biology   BNL