Skip to content

Commit cda6312

Browse files
author
haesleinhuepf
committed
regenerated docs
1 parent 67d6123 commit cda6312

27 files changed

+121
-18
lines changed

‎reference.md

+9
Original file line numberDiff line numberDiff line change
@@ -592,6 +592,9 @@ Takes a label map, determines for every label the maximum distance of any pixel
592592
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_labelMaximumExtensionRatioMap">labelMaximumExtensionRatioMap (Experimental)</a>
593593
Takes a label map, determines for every label the maximum distance of any pixel to the centroid and replaces every label with the that number.
594594

595+
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_labelMeanExtensionMap">labelMeanExtensionMap (Experimental)</a>
596+
Takes a label map, determines for every label the mean distance of any pixel to the centroid and replaces every label with the that number.
597+
595598
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_labelMeanIntensityMap">labelMeanIntensityMap (Experimental)</a>
596599
Takes an image and a corresponding label map, determines the mean intensity per label and replaces every label with the that number.
597600

@@ -785,6 +788,9 @@ Determines the mean average intensity projection of an image along Z.
785788
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_meanZProjectionAboveThreshold">meanZProjectionAboveThreshold (Experimental)</a>
786789
Determines the mean average intensity projection of an image along Z but only for pixels above a given threshold.
787790

791+
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_meanZProjectionBelowThreshold">meanZProjectionBelowThreshold (Experimental)</a>
792+
Determines the mean average intensity projection of an image along Z but only for pixels below a given threshold.
793+
788794
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_meanZProjectionBounded">meanZProjectionBounded</a>
789795
Determines the mean average intensity projection of an image along Z within a given z range.
790796

@@ -1282,6 +1288,9 @@ Computes a binary image with pixel values 0 and 1.
12821288
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_thresholdDefault">thresholdDefault</a>
12831289
The automatic thresholder utilizes the Default threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ 'Apply Threshold' method.
12841290

1291+
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_thresholdDoG">thresholdDoG (Experimental)</a>
1292+
Applies a Difference-of-Gaussian filter to an image and thresholds it with given sigma and threshold values.
1293+
12851294
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_thresholdHuang">thresholdHuang</a>
12861295
The automatic thresholder utilizes the Huang threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ 'Apply Threshold' method.
12871296

‎reference__binary.md

+3
Original file line numberDiff line numberDiff line change
@@ -268,6 +268,9 @@ Computes a binary image with pixel values 0 and 1.
268268
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_thresholdDefault">thresholdDefault</a>
269269
The automatic thresholder utilizes the Default threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ 'Apply Threshold' method.
270270

271+
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_thresholdDoG">thresholdDoG (Experimental)</a>
272+
Applies a Difference-of-Gaussian filter to an image and thresholds it with given sigma and threshold values.
273+
271274
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_thresholdHuang">thresholdHuang</a>
272275
The automatic thresholder utilizes the Huang threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ 'Apply Threshold' method.
273276

‎reference__filter.md

+3
Original file line numberDiff line numberDiff line change
@@ -361,6 +361,9 @@ Applies Gaussian blur to the input image and subtracts the result from the origi
361361
<a name="T"></a>
362362

363363
## T
364+
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_thresholdDoG">thresholdDoG (Experimental)</a>
365+
Applies a Difference-of-Gaussian filter to an image and thresholds it with given sigma and threshold values.
366+
364367
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_topHatBox">topHatBox</a>
365368
Applies a top-hat filter for background subtraction to the input image.
366369

‎reference__label.md

+3
Original file line numberDiff line numberDiff line change
@@ -139,6 +139,9 @@ Takes a label map, determines for every label the maximum distance of any pixel
139139
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_labelMaximumExtensionRatioMap">labelMaximumExtensionRatioMap (Experimental)</a>
140140
Takes a label map, determines for every label the maximum distance of any pixel to the centroid and replaces every label with the that number.
141141

142+
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_labelMeanExtensionMap">labelMeanExtensionMap (Experimental)</a>
143+
Takes a label map, determines for every label the mean distance of any pixel to the centroid and replaces every label with the that number.
144+
142145
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_labelMeanIntensityMap">labelMeanIntensityMap (Experimental)</a>
143146
Takes an image and a corresponding label map, determines the mean intensity per label and replaces every label with the that number.
144147

‎reference__measurement.md

+3
Original file line numberDiff line numberDiff line change
@@ -181,6 +181,9 @@ Takes a label map, determines for every label the maximum distance of any pixel
181181
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_labelMaximumExtensionRatioMap">labelMaximumExtensionRatioMap (Experimental)</a>
182182
Takes a label map, determines for every label the maximum distance of any pixel to the centroid and replaces every label with the that number.
183183

184+
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_labelMeanExtensionMap">labelMeanExtensionMap (Experimental)</a>
185+
Takes a label map, determines for every label the mean distance of any pixel to the centroid and replaces every label with the that number.
186+
184187
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_labelMeanIntensityMap">labelMeanIntensityMap (Experimental)</a>
185188
Takes an image and a corresponding label map, determines the mean intensity per label and replaces every label with the that number.
186189

‎reference__project.md

+3
Original file line numberDiff line numberDiff line change
@@ -52,6 +52,9 @@ Determines the mean average intensity projection of an image along Z.
5252
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_meanZProjectionAboveThreshold">meanZProjectionAboveThreshold (Experimental)</a>
5353
Determines the mean average intensity projection of an image along Z but only for pixels above a given threshold.
5454

55+
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_meanZProjectionBelowThreshold">meanZProjectionBelowThreshold (Experimental)</a>
56+
Determines the mean average intensity projection of an image along Z but only for pixels below a given threshold.
57+
5558
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_meanZProjectionBounded">meanZProjectionBounded</a>
5659
Determines the mean average intensity projection of an image along Z within a given z range.
5760

‎reference__segmentation.md

+3
Original file line numberDiff line numberDiff line change
@@ -49,6 +49,9 @@ Computes a binary image with pixel values 0 and 1.
4949
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_thresholdDefault">thresholdDefault</a>
5050
The automatic thresholder utilizes the Default threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ 'Apply Threshold' method.
5151

52+
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_thresholdDoG">thresholdDoG (Experimental)</a>
53+
Applies a Difference-of-Gaussian filter to an image and thresholds it with given sigma and threshold values.
54+
5255
### <img src="images/mini_empty_logo.png" width="18" height="18"/><img src="images/mini_clij2_logo.png" width="18" height="18"/><img src="images/mini_clijx_logo.png" width="18" height="18"/><a href="https://clij.github.io/clij2-docs/reference_thresholdHuang">thresholdHuang</a>
5356
The automatic thresholder utilizes the Huang threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ 'Apply Threshold' method.
5457

‎reference_averageDistanceOfNClosestNeighborsMap.md

+1-1
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33

44
Takes a label map, determines distances between all centroids and replaces every label with the average distance to the n closest neighboring labels.
55

6-
Categories: [Graphs](https://clij.github.io/clij2-docs/reference__graph), [Measurements](https://clij.github.io/clij2-docs/reference__measurement)
6+
Categories: [Graphs](https://clij.github.io/clij2-docs/reference__graph), [Labels](https://clij.github.io/clij2-docs/reference__label), [Measurements](https://clij.github.io/clij2-docs/reference__measurement)
77

88
### Usage in ImageJ macro
99
```

‎reference_averageNeighborDistanceMap.md

+1-1
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ Takes a label map, determines which labels touch and replaces every label with t
55

66
To determine the distances, the centroid of the labels is determined internally.
77

8-
Categories: [Graphs](https://clij.github.io/clij2-docs/reference__graph), [Measurements](https://clij.github.io/clij2-docs/reference__measurement)
8+
Categories: [Graphs](https://clij.github.io/clij2-docs/reference__graph), [Labels](https://clij.github.io/clij2-docs/reference__label), [Measurements](https://clij.github.io/clij2-docs/reference__measurement)
99

1010
### Usage in ImageJ macro
1111
```

‎reference_binaryAnd.md

+4
Original file line numberDiff line numberDiff line change
@@ -14,6 +14,10 @@ Categories: [Math](https://clij.github.io/clij2-docs/reference__math), [Binary](
1414
* <a href="reference_equal">equal</a> (2)
1515

1616

17+
### binaryAnd is often followed by
18+
* <a href="reference_release">release</a> (2)
19+
20+
1721
### Usage in ImageJ macro
1822
```
1923
Ext.CLIJ2_binaryAnd(Image operand1, Image operand2, Image destination);

‎reference_connectedComponentsLabelingBox.md

+1
Original file line numberDiff line numberDiff line change
@@ -20,6 +20,7 @@ Category: [Labels](https://clij.github.io/clij2-docs/reference__label)
2020
* <a href="reference_replaceIntensities">replaceIntensities</a> (3)
2121
* <a href="reference_maximumZProjection">maximumZProjection</a> (2)
2222
* <a href="reference_excludeLabelsOnEdges">excludeLabelsOnEdges</a> (2)
23+
* <a href="reference_release">release</a> (2)
2324
* <a href="reference_centroidsOfBackgroundAndLabels">centroidsOfBackgroundAndLabels</a> (2)
2425
* <a href="reference_maximum2DBox">maximum2DBox</a> (2)
2526
* <a href="reference_getMaximumOfAllPixels">getMaximumOfAllPixels</a> (2)

‎reference_detectMaxima3DBox.md

+4
Original file line numberDiff line numberDiff line change
@@ -8,6 +8,10 @@ higher intensity, and to 0 otherwise.
88

99
Categories: [Detection](https://clij.github.io/clij2-docs/reference__detection), [Binary](https://clij.github.io/clij2-docs/reference__binary)
1010

11+
### detectMaxima3DBox is often followed by
12+
* <a href="reference_release">release</a> (2)
13+
14+
1115
### Usage in ImageJ macro
1216
```
1317
Ext.CLIJ2_detectMaxima3DBox(Image source, Image destination, Number radiusX, Number radiusY, Number radiusZ);

‎reference_drawDistanceMeshBetweenTouchingLabels.md

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ Starting from a label map, draw lines between touching neighbors resulting in a
66
The end points of the lines correspond to the centroids of the labels. The intensity of the lines
77
corresponds to the distance between these labels (in pixels or voxels).
88

9-
Categories: [Graphs](https://clij.github.io/clij2-docs/reference__graph), [Measurements](https://clij.github.io/clij2-docs/reference__measurement)
9+
Categories: [Graphs](https://clij.github.io/clij2-docs/reference__graph), [Labels](https://clij.github.io/clij2-docs/reference__label), [Measurements](https://clij.github.io/clij2-docs/reference__measurement)
1010

1111
### Usage in ImageJ macro
1212
```

‎reference_drawMeshBetweenTouchingLabels.md

+1-1
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ Starting from a label map, draw lines between touching neighbors resulting in a
55

66
The end points of the lines correspond to the centroids of the labels.
77

8-
Categories: [Graphs](https://clij.github.io/clij2-docs/reference__graph), [Measurements](https://clij.github.io/clij2-docs/reference__measurement)
8+
Categories: [Graphs](https://clij.github.io/clij2-docs/reference__graph), [Labels](https://clij.github.io/clij2-docs/reference__label), [Measurements](https://clij.github.io/clij2-docs/reference__measurement)
99

1010
### Usage in ImageJ macro
1111
```

‎reference_drawTouchCountMeshBetweenTouchingLabels.md

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ Starting from a label map, draw lines between touching neighbors resulting in a
66
The end points of the lines correspond to the centroids of the labels. The intensity of the lines
77
corresponds to the touch count between these labels.
88

9-
Categories: [Graphs](https://clij.github.io/clij2-docs/reference__graph), [Measurements](https://clij.github.io/clij2-docs/reference__measurement)
9+
Categories: [Graphs](https://clij.github.io/clij2-docs/reference__graph), [Labels](https://clij.github.io/clij2-docs/reference__label), [Measurements](https://clij.github.io/clij2-docs/reference__measurement)
1010

1111
### Usage in ImageJ macro
1212
```

‎reference_erodeBox.md

+1
Original file line numberDiff line numberDiff line change
@@ -16,6 +16,7 @@ Categories: [Filter](https://clij.github.io/clij2-docs/reference__filter), [Bina
1616

1717

1818
### erodeBox is often followed by
19+
* <a href="reference_release">release</a> (2)
1920
* <a href="reference_binaryXOr">binaryXOr</a> (2)
2021
* <a href="reference_mask">mask</a> (4)
2122
* <a href="reference_dilateBox">dilateBox</a> (3)

‎reference_gaussianBlur3D.md

+1
Original file line numberDiff line numberDiff line change
@@ -11,6 +11,7 @@ Categories: Noise, [Filter](https://clij.github.io/clij2-docs/reference__filter
1111

1212
### gaussianBlur3D is often followed by
1313
* <a href="reference_subtractImages">subtractImages</a> (2)
14+
* <a href="reference_release">release</a> (2)
1415
* <a href="reference_thresholdDefault">thresholdDefault</a> (2)
1516
* <a href="reference_threshold">threshold</a> (4)
1617
* <a href="reference_thresholdOtsu">thresholdOtsu</a> (2)

‎reference_greaterConstant.md

+1-1
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@ Category: [Math](https://clij.github.io/clij2-docs/reference__math)
1212

1313

1414
### greaterConstant is often followed by
15-
* <a href="reference_release">release</a> (2)
15+
* <a href="reference_release">release</a> (3)
1616
* <a href="reference_mask">mask</a> (2)
1717
* <a href="reference_spotsToPointList">spotsToPointList</a> (2)
1818

‎reference_greaterOrEqual.md

+4
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,10 @@ f(a, b) = 1 if a >= b; 0 otherwise.
77

88
Category: [Math](https://clij.github.io/clij2-docs/reference__math)
99

10+
### greaterOrEqual is often followed by
11+
* <a href="reference_release">release</a> (2)
12+
13+
1014
### Usage in ImageJ macro
1115
```
1216
Ext.CLIJ2_greaterOrEqual(Image source1, Image source2, Image destination);

‎reference_labelMeanExtensionMap.md

+19
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,19 @@
1+
## labelMeanExtensionMap
2+
<img src="images/mini_empty_logo.png"/><img src="images/mini_empty_logo.png"/><img src="images/mini_clijx_logo.png"/>
3+
4+
Takes a label map, determines for every label the mean distance of any pixel to the centroid and replaces every label with the that number.
5+
6+
7+
8+
Categories: [Labels](https://clij.github.io/clij2-docs/reference__label), [Measurements](https://clij.github.io/clij2-docs/reference__measurement), Visualisation
9+
10+
### Usage in ImageJ macro
11+
```
12+
Ext.CLIJx_labelMeanExtensionMap(Image input, Image destination);
13+
```
14+
15+
16+
[Back to CLIJ2 reference](https://clij.github.io/clij2-docs/reference)
17+
[Back to CLIJ2 documentation](https://clij.github.io/clij2-docs)
18+
19+
[Imprint](https://clij.github.io/imprint)

‎reference_labelMeanIntensityMap.md

+1-1
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ Categories: [Labels](https://clij.github.io/clij2-docs/reference__label), [Measu
99

1010
### Usage in ImageJ macro
1111
```
12-
Ext.CLIJx_labelMeanIntensityMap(Image input, Input label_map, Image destination);
12+
Ext.CLIJx_labelMeanIntensityMap(Image input, Image label_map, Image destination);
1313
```
1414

1515

‎reference_labelSpots.md

+1-1
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ Categories: [Filter](https://clij.github.io/clij2-docs/reference__filter), [Labe
1414

1515
### labelSpots is often followed by
1616
* <a href="reference_labelVoronoiOctagon">labelVoronoiOctagon</a> (2)
17-
* <a href="reference_release">release</a> (4)
17+
* <a href="reference_release">release</a> (5)
1818
* <a href="reference_labelledSpotsToPointList">labelledSpotsToPointList</a> (7)
1919

2020

‎reference_maximumZProjection.md

+1-1
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@ Category: [Projections](https://clij.github.io/clij2-docs/reference__project)
1616

1717
### maximumZProjection is often followed by
1818
* <a href="reference_saveAsTIF">saveAsTIF</a> (2)
19-
* <a href="reference_release">release</a> (4)
19+
* <a href="reference_release">release</a> (16)
2020
* <a href="reference_copySlice">copySlice</a> (3)
2121

2222

0 commit comments

Comments
 (0)