The 3DRoiManager is a analysis plugin for 3D objects.
The image needs to be segmented and labelled before using it with 3DManager. You can use dedicated 3D segmentation tools like 3D Object Counter or Segmentation Editor. Alternatively you can use any thresholding tool in ImageJ (Adjust Threshold) then eventually use 3D morphological operation to improve segmentation. Then use the 3D Segmentation button in 3DManager to label existing objects in your binary image.
Once you have a 3D labelled image, you can import it to 3DManager using the Add Image button. If you have a Roi inside the image, only objects inside the Roi will be imported (whatever their Z position). The list of objects should appear in the left part of 3DManager. The default name is obj(number of object)-val(value in labelled image).
The objects can be selected as any list, right-click to select one object, Ctrl-click to add the object, Shift-click to select a range of objects. If you want to rename an object click the Rename button and enter the new name, if multiple objects are selected only the first one will be renamed.
If you want to delete an object from the list, simply click Delete. The Erase action will delete it from the list and draw black voxels in the active image, use with caution, only if you really want to delete an object from a labelled image.
If you want to merge multiple objects into one, click Merge, all selected objects will be fused to one object, actually the first one selected.
The Split in two procedure is experimental and will try to separate objects in two based on a watershed procedure. If the centres of the two computed new objects are too close, the object will not be separated, this minimal distance can be set up in 3DManager Options (the Settings icon at the bottom of 3D Manager).
The objects can be saved using the Save objects icon at the bottom of 3DManager, they can be then afterwards imported using the Load objects icon.
The contours of selected objects should be displayed as Rois in the current image. If not, simply check the Live Roi button. Note that if a great number of objects are selected the computing of the contours can be quite time consuming.
The Label button will add text overlay at objects position in the corresponding slice.
The Measure3D button will compute geometrical measurements on the selected objects, if no objects are selected, the measurements will be done for all objects. The various available measurements are available in the 3DManager options (Settings icon). The results table will show, you can then move the columns, or sort the rows based on a column. You can then save the values, and display the objects corresponding to the selected rows.
The Quantif3D button will compute intensity measurements on the selected objects, using active image. If no objects are selected, the measurements will be done for all objects. The various available measurements are available in the 3DManager options (Settings icon). The list of voxels with their intensity is available by clicking List Voxels. The results table will show, you can then move the columns, or sort the rows based on a column. You can then save the values, and display the objects corresponding to the selected rows.
Various distances measurements between two objects are available clicking the Distances button. If more than two objects are selected, all pairs will be processed. The label in the results table will display the processed pair. Note that two lines are used for one pair since some measurements are not symmetrical. The results table will show, you can then move the columns, or sort the rows based on a column. You can then save the values, and display the objects corresponding to the selected rows.
The angles are measured in 3D for three selected objects. The results will appear in the Log Window, three angles are computed in degrees, with each object the central object of the sector.
Selected objects can be draw in the current image stack using the Fill Stack button. This will all the voxels of the object in the current colour in the color picker. Note that the stack must be in RGB mode in order to obtain coloured objects.
The objects can also be displayed in 3D using the 3D Viewer plugin. The current colour will also be used.
All buttons and operations can be recorded, however we recommend you to first have a look to the Macro Functions available for 3DManager.