Nucleus segmentation
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NucleusJ a simple and user-friendly ImageJ plugin dedicated to the characterisation of nuclear morphology and chromatin organisation in 3D. NucleusJ quantifies parameters including shape and size of nuclei as well as intranuclear objects and their position within the nucleus. This documentation describes characteristics sorted by the nuclear segmentation step of NucleuJ 2.0. 19 characteristics are produced and listed in this documentation. The documentation explains how to launch the plugin, how to call the input dataset and how to produce the output files. Parameters of the plugin are scalable through a configuration file (config file). NucleusJ 2.0 includes two different segmentation methods hereafter named Otsu modified method and gift-wrapping method.
First click on Segmentaion NucleusJ 2 in NucleusJ2.0 plugin menu :
Then choose folder containing one or several images of nucleus you want to segment as input folder and an output folder in the following window :
And finally click on start to run the segmentation analysis
Results are composed of two folder :
-
Otsu folder containing images segmented by OTSU threshold method, in 8bits
-
GIFT folder containing images segmented by Gift-wrapping method
In addition to the segmented images in the 2 folders a file name result_Segmentation_Analyse.csv is generated. This tabulated file contains the computed parameters useful for morphological nuclear description. Here follows the list of parameters:
| Parameter name | Description |
|---|---|
| NucleusFileName | Nucleus image file name |
| Volume | Volume of segmented object (sum of white voxels) |
| Flatness | Computed by ratio between major and minor axes of the segmented object |
| Elongation | Computed by ratio between major and medium axes of the object |
| Sphericity | Computed by ratio between surface area and volume |
| Esr | Equivalent spherical radius, estimated radius computed from the volume |
| SurfaceArea | Segmented object surface area |
| MeanIntensityNucleus | Mean voxels intensity of segmented image |
| MeanIntensityBackground | Mean intensity of the background |
| StandardDeviation | Standard deviation of the segmented object intensity |
| MinIntensity | Minimum voxel intensity of the segmented object |
| MaxIntensity | Maximum voxel intensity of the segmented object |
| MedianIntensityImage | Median voxel intensity of raw image |
| MedianIntensityNucleus | Median voxel intensity of segmented object |
| MedianIntensityBackground | Median voxel intensity of background |
| ImageSize | Number of voxel |
| OTSUThreshold | OTSU threshold used to segment the image |
By default there is a list of parameters defined (see next table). Example of parameters modification in graphical interface :
The following window show how edit parameters :
Description of the editable parameters:
| Parameter name | Default value | Value type | Corresponding number in user interface | Description |
|---|---|---|---|---|
| minVolumeNucleus | 1 | Int | 1 | Minimum volume of detected object |
| maxVolumeNucleus | 3000000 | Int | 2 | Maximum volume of detected object |
| GiftWrapping | True | Boolean | 3 | Gift wrapping activation |
| xcal | 1 | Double | 4 | X calibration value |
| ycal | 1 | Double | 5 | Y calibration value |
| zcal | 1 | Double | 6 | Z calibration value |
If a special parameter configuration is needed/necessary, a config file can be used. A config file can be selected before analyzing :
Config file is text file containing 1 parameter per line composed of ParameterName:ParameterValue.In this example, the minimum and maximum volume size detected object are modified :