Graph-Assistant =============== 05-Aug-2017 fixed wrong error bars when columns were only filled partially 07-Mar-2016 made compatible for ImageJ > 1.48 26-Aug-2011 12:30 The Graph-Assistant is a macro file that adds plotting facilities to an ObjectJ project without being part of the ObjectJ embedded macros. It is a separate file named "Graph-Assistant.txt". It can be installed by dragging the file from the Finder/Explorer onto the ImageJ main window. After installation, a little "GA" tool icon becomes visible in the ImageJ main window. Creating a plot: ================ Click on the "GA" icon to create a plot. Currently, several menu items like "Dia" and "FluorTotal" are available for the creation of scatter plots. These indicate the columns whose entries are used as yValues. Column "Axis" is used for the xValues (cell length) in all cases. The plot listens to the current Qualifier settings. Any previous plot with the same name will be deleted before it is re-created. Confidence intervals: ====================== If "useErrorBars" = true, the plot includes confidence intervals for 95% as "error bars" with adjustable bin width. Choose "List" in the plot to observe the error bars in numerical format. Logarithmic x-Axis: =================== You can choose the x-axis to be logarithmic: activate the ImageJ window, keep the alt key down, and choose the corresponding plot from the GA icon. Use Roi for Qualifying: ====================== With a scatter plot in front, create any roi to limit qualification to spots within the roi, then choose GA>Qualify Roi. You cannot subsequently narrow the selection by repeatedly choosing Qualify_ROI. However, you can use the shift key for adding and the alt key for subtracting a roi, resulting in a roi that is composite, disjunct, or contains holes. Disqualify_ROI has inverse effect. "Qualify_All" qualifies all cells without repainting the current plot. Subsequent (map-) operations will listen to the new qualifying pattern; e.g. you could completely delete (dis-)qualified objects via menu ObjectJ>Objects>Delete Objects.. Saving a Roi for Qualifying: You can save any plot together with its roi as ".tif" format, and re-use that file later for qualifying. No automatic delete/repaint is done if title ends with ".tif". Saving a plot for documentation is peferably done in ".png" format. Editing and re-loading the Graph-Assistant ========================================== The Graph-Assistant will be re-installed whenever you choose "ObjectJ> Show Embedded Macros>" and subsequently click "Install in ObjectJ Menu". If the ObjectJ menu shows an item "Load Graph-Assistant", you also may use that for (re-)installing. If "Graph-Assistant.txt" is shown as front window in ImageJ, you can install it via menu Macros> Install. In this case, the name and location of the file can be arbitrary. Similarly, you can drag any text file that has been edited in an external Editor (such as Text Wrangler) onto the ImageJ window in order to install it. If you choose a different macro toolset by clicking on the right-most tool icon ">>", the GA icon will be uninstalled. You will have to re-install it as indicated above.