Object Analyzer components reference
This section describes the components of the Object Analyzer (OA) in Huygens. This section provides an overview, for details on how to use all Object Analyzer please see the introductory and expert tutorials.
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# Conditions: pipe 0 chan 0: thresh 504.8, seed 540.52, garb. 1, objects 12. ROI: vol 1103 um^3, CM (130, 115, 10)
The parameters about the ROI (volume and CM) are the same for both pipes, in case two are active. This is because there is only one ROI for all pipes and channels, and the Center Of Mass (CM) here reported is calculated considering the ROI as a uniform, solid object.
There is another way to calculate the CM of the ROI, not considering it homogeneous but taking into account the real image intensities in envelops. These intensities, being different per pipe, yield to different ROI's CM per pipe. This is not reported in the conditions rows, but as object rows in the table when you select Analyze all. In this case, the ROI itself is treated as a new object in each pipe and more detailed information is reported in separate rows in the table. See the ROI wiki article.
22. The table rows, how to explore them
Each row in the table is either a Conditions report (see 21) or information about one of the segmented objects.
In the second case, the object the row refers to is identified by some mandatory parameters (parameters that are always reported):
- Label: an integer index that is unique, per object, inside its pipe.
- Chan: the image channel this object belongs to
- Surf: the surface pipe in the current analysis the object belongs to (P = Primary, S = Secondary).
- Voxels: the number of VoXels in that object
- C.Mass: three columns (X, Y, Z) for the Center Of Mass location of the object, in the image coordinate system, with VoXels as units.
The second letter in the Surf. column informs whether the object you clicked was in the front (F) or the back (B) position. This is only relevant in the following situation: it may happen that two objects in different pipes overlap in space (or they apparently do from the current point of view) and when you click somewhere on the screen you are actually selecting both of them, if the pipe interaction mode is PS or All (6). In that case, two rows are added to the table, and this second letter lets you know which of the two was in front of the other, from the current point of view.
By moving the mouse over the table rows the corresponding object is highlighted on the canvas (11). Objects in the Primary pipe are highlighted in red, and objects in the Secondary pipe in green.
A good way to find an object in a very long table is by clicking on it on the rendering canvas while the 'Analyze object' mode is active: the table will be shifted to show its corresponding row, and it will be highlighted.
When you move over the table cells the current value is shown on the tooltip bar at the bottom (23). This, combined with the selection of rows (see below) or columns (20), allows a quick exploration of the table and the comparison of different parameter values.
In the following example, when you move the cursor over one cell that contains the distance to the first neighbor, you can see the following in the tooltip: -+38/S 1NP.CMCM: 4.2358+-. The first part is the label of the object in the current row: label 38 on the Secondary pipe. Then the parameter tag
1NP.CMCMrefers to the CM-to-CM distance between this object and the nearest object in the other pipe. Then comes the distance itself: 4.23 microns.
The nice thing of that tooltip region is that it can show not only the information of the cell pointed by the mouse, which would not be really useful, but also other values that can be set as reference. Try this: while keeping the Control (Ctrl) key pressed on the keyboard, select a couple of rows by clicking on the row number at the very left of the table. The selected rows will turn green. If you now hover the mouse over a cell on any other row, you will get the value not only of that cell, but also those in the corresponding cells of the selected objects (rows). This is a quick way to compare results for different objects that can be distant in the table.
If you select columns instead of rows in the table the tooltip will display the corresponding parameter values for the same object (see 20). Do not highlight columns and rows at the same time by now: it may be too confusing to interpret!!!
23. The status bar and tooltip
The bottom part of the window is a status bar that also shows an contextual tooltip.
The left side reports the current status of the renderer and analyzer. You can see whether a long computation is running or if the analyzer is ready for further interaction.
Then the current size of the canvas is reported. When you first start the OA, the canvas size is adapted to the exact room left for the scene rendering, but it can be larger or smaller at wish. See Top menu (1) > Options > Virtual render size.
The 'Dragging' status refers to the automatic rendering of the scene while the user interacts with it. In very slow systems, the dragging is turned off automatically and the rendering only happens after the user released the mouse buttons or finished moving the segmentation sliders.
The tooltip (the region with light yellow background) shows contextual information:
- A longer description of the reported parameters when you hover over the table headers and a sum of the cell below them (see 20)
- The value in the cell under the cursor when you point at table rows, plus selected reference values (see 20 and 22)
- The different actions bound to the mouse buttons, when the cursor is inside the rendering canvas