Skip to content

Commit 7836ba5

Browse files
elevanselevans
committed
Add labeling/result table output section
Add a new output section describing what the outputs are.
1 parent 457dd94 commit 7836ba5

1 file changed

Lines changed: 25 additions & 1 deletion

File tree

‎docs/ops/doc/examples/labeling_mesh.rst‎

Lines changed: 25 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -25,12 +25,13 @@ To use the script in the example first download the sample dataset `here`_. Next
2525
where you can customize some values to your own data, such as the channel names, channel position and image calibration values.
2626

2727
.. figure:: https://media.scijava.org/scijava-ops/1.0.1/labeling_mesh_example_dialog.png
28+
:align: center
2829

2930
Once the script has been configured click **OK** to start the analysis. The script will display two tables (one for each channel with the given channel name) and the labeling
3031
output for the puncta within nuclear regions only.
3132

3233
.. figure:: https://media.scijava.org/scijava-ops/1.0.1/labeling_mesh_example_1.gif
33-
34+
:align: center
3435

3536
Results of 3D nuclear puncta segmentation on the sample data.
3637

@@ -60,6 +61,29 @@ and a pixel width and height of 0.0650 μm with a step size of 0.1 μm (see the
6061
| Voxel depth (μm) | 0.1000 |
6162
+--------------------+---------+
6263

64+
65+
Labeling output and result tables
66+
---------------------------------
67+
68+
After the script completes two results tables will be displayed, one for each channel respectively. Each table contains measurements for the **size** of the label, the **volume** and the **sphericity**. Both the volume and sphericity Ops
69+
work on mesh objects, while the size Op works on the sample itself.
70+
71+
.. figure:: https://media.scijava.org/scijava-ops/1.0.1/labeling_mesh_example_result_tables.png
72+
:align: center
73+
74+
The output result tables for the "Vif" and "Nuclei" channels.
75+
76+
In addition to the result tables, the label imdage (also known as an *index image*) of the channel "A" data extracted from channel "B" regions is shown. Note that these labels are 3D (XYZ) and are used to create meshes for the geometry measurements.
77+
78+
79+
.. figure:: https://media.scijava.org/scijava-ops/1.0.1/labeling_mesh_example_2.gif
80+
:width: 65%
81+
:align: center
82+
83+
The output label image with "3-3-2 RGB" LUTs applied in Fiji.
84+
85+
**Please note that this script can take upwards of 2-3 minutes to run!**
86+
6387
.. tabs::
6488

6589
.. code-tab:: python

0 commit comments

Comments
 (0)