KEYWORD Window Coordinates Method MaximumIntensity Box Range LastPoint NextPoint TotalPoints DeleteGroup DeleteLast GetDistances OpenFile SingleColumn AutoSave AutoPurge SaveDistances DistancesSaved InsertText DESCRIPTION The Distance tool helps you to measure distances and optionally record them to a file. As an example, here is how you could measure the distance between two arbitrary points in a dataset: 1) Enter the number for the window of interest in the Window field. 2) From the menu next to the Window field, select "real space" if you want the distances reported to factor in the pixel spacing; select "data coords" if you want the distances reported to be in pixels. 3) Select "every two" from the second menu to the right of the Window field. 4) Move the mouse cursor to the first point of interest in the window. Click on the left mouse button. The coordinates for the point will be displayed in the scrolling window in the Distance tool. Repeat for the second point. Again the coordinates for the point will be displayed in the scrolling window; the distance between the points will also appear there. Window Use this field to enter the number of the window in which you want measurements. Coordinates The menu next to the Window field controls which coordinate system is used when determining the distances. When the real coordinates are used, the coordinates of the points take into account the pixel spacing, origin, and tilt angles recorded in the image header, and the distances reported will have the same units as the pixel spacings (this is usually microns for optical microscope data). When the data coordinates are used, the coordinates and distances reported are in pixels. Method The second menu to the right of the Window field controls how the distances are calculated from the points picked in a window: compare any num Pick as many points as you want. Then press the get distances button to report the distances for every pair of points in the set. continuous Every time a point is selected, the distance between it and the last point picked will be reported. Pressing the get distances button will report the distance between the last two points selected. every two For every two points selected, the distance between them is reported so if you select four points, the distance between the first and second and the third and fourth points is printed. Pressing the get distances button will report the distance between the last two selected points if an even number of points have been selected so far; otherwise it will generate a blank line. manual Every time a point is selected, the point given in the Next Point field is replaced and the distance between the newly selected point and the other point (point one if the next point was zero or point zero if the next point was one) is reported. MaximumIntensity When the "max intens" toggle is on, the program will do a local search for the maximum intensity and use that point for calculating distances rather than the point where the mouse was clicked. The values in the Box and Range fields control how the search is done. Box If the max intens toggle is on, the search for the maximum intensity is done in the image data after it has been smoothed with a two-dimensional mean filter whose width in pixels is given in the Box field. No smoothing is done for box sizes less than three. Range Let r be the value show in the Range field. If the max intens toggle is on, the point that is used for distance calculations will be at most r pixels in x and at most r pixels in y from the point of the mouse click. LastPoint The values in these fields are updated each time a point is selected. The first field displays the index of the point; this will be between zero and the total number of points minus one. The second field displays the coordinates of the point. NextPoint This field displays the point number which will be updated when a point is picked. If this value is equal to the total number of points, a new point will be added; otherwise the newly selected point replaces the one with the given point number. The next point can be changed by entering a value or using the arrow buttons next to the field. TotalPoints This field displays the total number of points that have been picked for the current group. DeleteGroup Pressing the "del group" button purges all the points currently picked and resets for the next group of points to be picked. DeleteLast Pressing the "del last pt" button deletes the last point. GetDistances Pressing this button causes a measurement to be made between the currently selected points. This is only necessary when using the "compare any num" method. For the other methods the distance is measured automatically. The result of the measurement is shown in the scrolled area, and if a file is currently open and the autosave toggle is on, the result will also be written to the file. OpenFile To save distances to a file, open the file before you start taking measurements. To do this, press the "Open File" button to select the file or enter the file name directly into into the field next to the "Open File" button. When you are finished making the distance file, close it if you wish to continue using the distance program without adding any more to that file. SingleColumn If you are going to generate more than about 10 distances in one measurement set, you probably want to send the output to a single column. Do this by turning on the "single column" toggle before you begin to save measurements. When the "single column" toggle is off, distances from one measurement are saved in separate columns on the same line. AutoSave When the autosave toggle is on and a file is open, any measurement (whether it occurs automatically when using the continuous, "every two", or manual methods or is initiated by pressing the "get distances" button) is written to the file. AutoPurge When the autopurge toggle is on and distances are written to a file, the current set of points will be purged so you can start on a new set. When this toggle is off, you must press the "del group" button to start a new set of points. SaveDistances Pressing the "save distances button" while a file is open will append the distance measurement(s) for the currently selected points to that file. DistancesSaved This field displays the number of distance measumrents that have been saved to the currently open file. InsertText Each time you click the Insert Text button, the characters in the adjacent field will be inserted in the output file. This lets you separate sets of distances in one file if needed.