Calculate mean signal intensity within regions of
interest (ROI), as well as the area of each ROI.
This command has three variants, standard (Region Statistics),
multi-channel (Region Stats (multi-chan)), and
multi-channel with threshold exclusion (Region Stats (excl. thresh.),
with different structures for input parameters and results.
Expects arbitrary bit-depth images with between 1 and 3 channels. Channels are assumed to be in red, green, blue order.
Type: Image File (imagej.data.Dataset)
Set of ROIs defining the regions for which statistics will be calculated.
Type: ROI Set (file) (imagej.data.overlay.AbstractOverlay[])
Integers specifying thresholds for each channel. The appropriate threshold is subtracted from each pixel value. If the pixel value is less than the threshold, the pixel value is counted as 0.
Type: Numeric (double)
Flag specifying whether pixel values should be measured
above the threshold (false, default) or below the
threshold (true).
Type: Logical (boolean)
One result row is produced for each ROI.
Mean of threshold-subtracted pixel values within the ROI. For green and blue totals, returns 0 if the image does not include a second or third channel.
If Invert is false (default):
∑[max(Xi,c - Tc, 0)] / area
If Invert is true:
–∑[min(Xi,c - Tc, 0)] / area
Xi,c, value at pixel i on channel c
Tc, threshold for channel c
Type: Numeric (double)
Number of pixels within the ROI.
Type: Integer (int)
Expects arbitrary bit-depth images with any number of channels.
Type: Image File (imagej.data.Dataset)
Set of ROIs defining the regions for which statistics will be calculated.
Type: ROI Set (file) (imagej.data.overlay.AbstractOverlay[])
A space-separated ordered list of thresholds for each channel. The appropriate threshold is subtracted from each pixel value. If the pixel value is less than the threshold, the pixel value is counted as 0.
For example, 10 25 102 would specify a threshold of 10 for the first
channel, a threshold of 25 for the second channel, and a threshold of 102
for the third channel. If an image has fewer channels than
the number of thresholds listed, the extra threshold values will not
be used. If an image has more channels than the number of thresholds
listed, they will be recycled in order. If no thresholds are listed,
a threshold of 0 is implied.
Type: Text (String)
Flag specifying whether pixel values should be measured
above the threshold (false, default) or below the
threshold (true).
Type: Logical (boolean)
One result row is produced for each image channel within each ROI.
Mean of threshold-subtracted pixel values of a single channel within the ROI.
If Invert is false (default):
∑[max(Xi,c - Tc, 0)] / area
If Invert is true:
–∑[min(Xi,c - Tc, 0)] / area
Xi,c, value at pixel i on channel c
Tc, threshold for channel c
Type: Numeric (double)
0-based index of the image channel measured.
Type: Integer (int)
Number of pixels within the ROI.
Type: Integer (int)
This variation of the multi-channel region statistics command
(Region Stats (multi-chan)) excludes pixels below the threshold, rather
than subtracting threshold values from the data. Thus, all pixels below
the threshold are ignored, rather than counted as 0.
Expects arbitrary bit-depth images with any number of channels.
Type: Image File (imagej.data.Dataset)
Set of ROIs defining the regions for which statistics will be calculated.
Type: ROI Set (file) (imagej.data.overlay.AbstractOverlay[])
A space-separated ordered list of thresholds for each channel. Pixels below the threshold (greater than if invert is true) are ignored and do not contribute to the mean value or area measurements.
Note that thresholds are considered separately for each channel. For example,
if the specified threshold is 10 25 102, a pixel with values of 100 on each
channel will be counted in the statistics computed for channels 1 and 2, but
will not be counted in the statistics computed for channel 3.
If an image has fewer channels than the number of thresholds listed,
the extra threshold values will not be used. If an image has more channels
than the number of thresholds listed, they will be recycled in order. If no
thresholds are listed, a threshold of 0 is implied.
Type: Text (String)
Flag specifying whether pixel values should be measured
above the threshold (false, default) or below the
threshold (true).
Type: Logical (boolean)
One result row is produced for each image channel within each ROI.
Mean of pixel values above the threshold of a single channel within the ROI.
If no pixels are above the threshold, the result is -1.
Type: Numeric (double)
0-based index of the image channel measured.
Type: Integer (int)
Number of pixels above the threshold within the ROI.
Type: Integer (int)
