To start using it, switch to High Contrast to see what areas fall above or below threshold. Adjust the threshold to the proper level to segment your features of interest, switching back and forth between Regular and High contrast as needed. High Contrast uses the second color ramp, so you can toggle between these views easily by using hot key F9 to switch back to the first ramp, and hot key F10 to switch from the first to the second ramp. Select the Alternate mouse to use the mouse buttons to control the filling operation. Then click on the interior of a desired area to flood that area in red. Adjust the area if necessary then press the Build button or the B hot key to build a contour around the area.
If you are in High Contrast mode, you should turn off the Float button in the 3dmod Information window unless you want the threshold from change when you go from section to section.
Image data are always analyzed as 8-bit bytes, even when they have been loaded into the program as 16-bit integers. In the latter case, the current setting of the Low and High sliders in the Information window determines how data are scaled to bytes. For best results, be sure that the Low and High sliders are set so that images have a good contrast with a fairly wide range between the Black and White sliders. Using the autocontrast function generally leaves the sliders in positions that will allow good scaling for autocontouring. Note that the threshold setting changes it meaning when the Low and High sliders are changed.
If you find that you can obtain usable contours with this approach, you can run the same operation on a defined region of the image stack using Imodauto. A given threshold should have the same effect with that program as in this window, provided that data are loaded with the same intensity scaling. The scaling will be the same by default, but if you set the scaling when loading data into 3dmod, you will need to use the same scaling when running Imodauto. However, if data are loaded into the program as 16-bit integers, use the setting of the Low and High sliders as the scaling values when running Imodauto.
Smoother contours may be obtained by applying smoothing in the image processing window. To use this approach, select the smoothing panel and try different sigma values. Be sure to uncheck Rescale to match min/max so that the smoothed data will have consistent intensities from section to section, and will correspond to the intensity values if you use smoothing in Imodauto. You can check Autoapply to have the smoothing happen automatically when you go from one section from the next.