Fix organization of tutorial notebooks

With 7da16b4 they were reorganized, but many of the links were not fixed. This commit cleans things up so that everything is consistently linked again. It also removes incomplete "aspirational" notebooks, in favor of only useful content.
imagej · Sep 10, 2020 · d3ff8e8 · d3ff8e8
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Showing 109 changed files with 15 additions and 202 deletions.
diff --git a/...ooks/2-ImageJ-Basics/1-Fundamentals.ipynb → ...books/1-Using-ImageJ/1-Fundamentals.ipynb b/...ooks/2-ImageJ-Basics/1-Fundamentals.ipynb → ...books/1-Using-ImageJ/1-Fundamentals.ipynb
@@ -175,7 +175,7 @@
     "### Comparison with ImageJ 1.x\n",
     "<div style=\"float: left\"><img src=\"http://imagej.net/_images/a/a8/Imagej1-icon.png\" width=\"48\"></div>\n",
     "\n",
-    "[ImageJ 1.x](https://imagej.net/ImageJ1) has a similar concept with the `ij.ImageJ` class, which is created using `new ImageJ()` and cached statically as a singleton.  This allows the ImageJ instance to be recovered later by calling `IJ.getInstance()`, and simplifies the API in some ways.  However, the assumption that there will only ever be one ImageJ per JVM limits its flexibility, and the fact that `ij.ImageJ` extends `java.awt.Frame` makes ImageJ 1.x difficult to use [headless](https://imagej.net/Headless) or with user interfaces other than Java AWT. Furthermore, [ImageJ 1.x](https://imagej.net/ImageJ1) is not service-driven, which makes it less extensible; see the <a href=\"../3-Advanced-Usage/1-SciJava-in-Detail.ipynb\">SciJava in Detail</a> tutorial notebook for more information."
+    "[ImageJ 1.x](https://imagej.net/ImageJ1) has a similar concept with the `ij.ImageJ` class, which is created using `new ImageJ()` and cached statically as a singleton.  This allows the ImageJ instance to be recovered later by calling `IJ.getInstance()`, and simplifies the API in some ways.  However, the assumption that there will only ever be one ImageJ per JVM limits its flexibility, and the fact that `ij.ImageJ` extends `java.awt.Frame` makes ImageJ 1.x difficult to use [headless](https://imagej.net/Headless) or with user interfaces other than Java AWT. Furthermore, [ImageJ 1.x](https://imagej.net/ImageJ1) is not service-driven, which makes it less extensible; see the <a href=\"../3-Advanced-Topics/1-SciJava-in-Detail.ipynb\">SciJava in Detail</a> tutorial notebook for more information."
    ]
   },
   {
@@ -710,7 +710,7 @@
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+   "version": "2.5.6"
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diff --git a/notebooks/2-ImageJ-Basics/2-ImageJ-Ops.ipynb → notebooks/1-Using-ImageJ/2-ImageJ-Ops.ipynb b/notebooks/2-ImageJ-Basics/2-ImageJ-Ops.ipynb → notebooks/1-Using-ImageJ/2-ImageJ-Ops.ipynb
@@ -2778,7 +2778,7 @@
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-   "version": "2.4.3"
+   "version": "2.5.6"
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diff --git a/...ks/2-ImageJ-Basics/3-ImgLib2-Basics.ipynb → ...oks/1-Using-ImageJ/3-ImgLib2-Basics.ipynb b/...ks/2-ImageJ-Basics/3-ImgLib2-Basics.ipynb → ...oks/1-Using-ImageJ/3-ImgLib2-Basics.ipynb
diff --git a/notebooks/2-ImageJ-Basics/4-Tables.ipynb → notebooks/1-Using-ImageJ/4-Tables.ipynb b/notebooks/2-ImageJ-Basics/4-Tables.ipynb → notebooks/1-Using-ImageJ/4-Tables.ipynb
diff --git a/...ImageJ-Basics/5-Mixed-World-ImageJ1.ipynb → ...-Using-ImageJ/5-Mixed-World-ImageJ1.ipynb b/...ImageJ-Basics/5-Mixed-World-ImageJ1.ipynb → ...-Using-ImageJ/5-Mixed-World-ImageJ1.ipynb
diff --git a/...-ImageJ/6-ImageJ-with-Python-Kernel.ipynb → ...-ImageJ/6-ImageJ-with-Python-Kernel.ipynb b/...-ImageJ/6-ImageJ-with-Python-Kernel.ipynb → ...-ImageJ/6-ImageJ-with-Python-Kernel.ipynb
diff --git a/...ooks/3-Extending-ImageJ/1-Scripting.ipynb → ...ageJ/7-Calling-Scripts-from-Scripts.ipynb b/...ooks/3-Extending-ImageJ/1-Scripting.ipynb → ...ageJ/7-Calling-Scripts-from-Scripts.ipynb
@@ -112,7 +112,7 @@
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    "name": "Groovy",
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diff --git a/...books/4-Using-Ops/examples/copy/img.ipynb → notebooks/1-Using-ImageJ/Ops/copy/img.ipynb b/...books/4-Using-Ops/examples/copy/img.ipynb → notebooks/1-Using-ImageJ/Ops/copy/img.ipynb
diff --git a/...-Ops/examples/copy/iterableInterval.ipynb → ...ng-ImageJ/Ops/copy/iterableInterval.ipynb b/...-Ops/examples/copy/iterableInterval.ipynb → ...ng-ImageJ/Ops/copy/iterableInterval.ipynb
diff --git a/...books/4-Using-Ops/examples/copy/rai.ipynb → notebooks/1-Using-ImageJ/Ops/copy/rai.ipynb b/...books/4-Using-Ops/examples/copy/rai.ipynb → notebooks/1-Using-ImageJ/Ops/copy/rai.ipynb
diff --git a/...ing-Ops/examples/filtering/addNoise.ipynb → .../1-Using-ImageJ/Ops/filter/addNoise.ipynb b/...ing-Ops/examples/filtering/addNoise.ipynb → .../1-Using-ImageJ/Ops/filter/addNoise.ipynb
diff --git a/.../examples/filtering/addPoissonNoise.ipynb → ...g-ImageJ/Ops/filter/addPoissonNoise.ipynb b/.../examples/filtering/addPoissonNoise.ipynb → ...g-ImageJ/Ops/filter/addPoissonNoise.ipynb
diff --git a/...ng-Ops/examples/filtering/bilateral.ipynb → ...1-Using-ImageJ/Ops/filter/bilateral.ipynb b/...ng-Ops/examples/filtering/bilateral.ipynb → ...1-Using-ImageJ/Ops/filter/bilateral.ipynb
diff --git a/.../examples/filtering/derivativeGauss.ipynb → ...g-ImageJ/Ops/filter/derivativeGauss.ipynb b/.../examples/filtering/derivativeGauss.ipynb → ...g-ImageJ/Ops/filter/derivativeGauss.ipynb
diff --git a/.../4-Using-Ops/examples/filtering/dog.ipynb → ...books/1-Using-ImageJ/Ops/filter/dog.ipynb b/.../4-Using-Ops/examples/filtering/dog.ipynb → ...books/1-Using-ImageJ/Ops/filter/dog.ipynb
diff --git a/...-Using-Ops/examples/filtering/gauss.ipynb → ...oks/1-Using-ImageJ/Ops/filter/gauss.ipynb b/...-Using-Ops/examples/filtering/gauss.ipynb → ...oks/1-Using-ImageJ/Ops/filter/gauss.ipynb
diff --git a/...sing-Ops/examples/filtering/hessian.ipynb → ...s/1-Using-ImageJ/Ops/filter/hessian.ipynb b/...sing-Ops/examples/filtering/hessian.ipynb → ...s/1-Using-ImageJ/Ops/filter/hessian.ipynb
diff --git a/...4-Using-Ops/examples/filtering/ifft.ipynb → ...ooks/1-Using-ImageJ/Ops/filter/ifft.ipynb b/...4-Using-Ops/examples/filtering/ifft.ipynb → ...ooks/1-Using-ImageJ/Ops/filter/ifft.ipynb
diff --git a/.../4-Using-Ops/examples/filtering/max.ipynb → ...books/1-Using-ImageJ/Ops/filter/max.ipynb b/.../4-Using-Ops/examples/filtering/max.ipynb → ...books/1-Using-ImageJ/Ops/filter/max.ipynb
diff --git a/...4-Using-Ops/examples/filtering/mean.ipynb → ...ooks/1-Using-ImageJ/Ops/filter/mean.ipynb b/...4-Using-Ops/examples/filtering/mean.ipynb → ...ooks/1-Using-ImageJ/Ops/filter/mean.ipynb
diff --git a/...Using-Ops/examples/filtering/median.ipynb → ...ks/1-Using-ImageJ/Ops/filter/median.ipynb b/...Using-Ops/examples/filtering/median.ipynb → ...ks/1-Using-ImageJ/Ops/filter/median.ipynb
diff --git a/.../4-Using-Ops/examples/filtering/min.ipynb → ...books/1-Using-ImageJ/Ops/filter/min.ipynb b/.../4-Using-Ops/examples/filtering/min.ipynb → ...books/1-Using-ImageJ/Ops/filter/min.ipynb
diff --git a/...ing-Ops/examples/filtering/padInput.ipynb → .../1-Using-ImageJ/Ops/filter/padInput.ipynb b/...ing-Ops/examples/filtering/padInput.ipynb → .../1-Using-ImageJ/Ops/filter/padInput.ipynb
diff --git a/...xamples/filtering/partialDerivative.ipynb → ...ImageJ/Ops/filter/partialDerivative.ipynb b/...xamples/filtering/partialDerivative.ipynb → ...ImageJ/Ops/filter/partialDerivative.ipynb
diff --git a/...-Using-Ops/examples/filtering/sigma.ipynb → ...oks/1-Using-ImageJ/Ops/filter/sigma.ipynb b/...-Using-Ops/examples/filtering/sigma.ipynb → ...oks/1-Using-ImageJ/Ops/filter/sigma.ipynb
diff --git a/...-Using-Ops/examples/filtering/sobel.ipynb → ...oks/1-Using-ImageJ/Ops/filter/sobel.ipynb b/...-Using-Ops/examples/filtering/sobel.ipynb → ...oks/1-Using-ImageJ/Ops/filter/sobel.ipynb
diff --git a/...ing-Ops/examples/filtering/tubeness.ipynb → .../1-Using-ImageJ/Ops/filter/tubeness.ipynb b/...ing-Ops/examples/filtering/tubeness.ipynb → .../1-Using-ImageJ/Ops/filter/tubeness.ipynb
diff --git a/...ing-Ops/examples/filtering/variance.ipynb → .../1-Using-ImageJ/Ops/filter/variance.ipynb b/...ing-Ops/examples/filtering/variance.ipynb → .../1-Using-ImageJ/Ops/filter/variance.ipynb
diff --git a/...s/4-Using-Ops/examples/segment/help.ipynb → notebooks/1-Using-ImageJ/Ops/help.ipynb b/...s/4-Using-Ops/examples/segment/help.ipynb → notebooks/1-Using-ImageJ/Ops/help.ipynb
diff --git a/...s/4-Using-Ops/examples/labeling/cca.ipynb → ...oks/1-Using-ImageJ/Ops/labeling/cca.ipynb b/...s/4-Using-Ops/examples/labeling/cca.ipynb → ...oks/1-Using-ImageJ/Ops/labeling/cca.ipynb
diff --git a/...Ops/examples/morphology/blackTopHat.ipynb → ...g-ImageJ/Ops/morphology/blackTopHat.ipynb b/...Ops/examples/morphology/blackTopHat.ipynb → ...g-ImageJ/Ops/morphology/blackTopHat.ipynb
diff --git a/...Using-Ops/examples/morphology/close.ipynb → ...1-Using-ImageJ/Ops/morphology/close.ipynb b/...Using-Ops/examples/morphology/close.ipynb → ...1-Using-ImageJ/Ops/morphology/close.ipynb
diff --git a/...sing-Ops/examples/morphology/dilate.ipynb → ...-Using-ImageJ/Ops/morphology/dilate.ipynb b/...sing-Ops/examples/morphology/dilate.ipynb → ...-Using-ImageJ/Ops/morphology/dilate.ipynb
diff --git a/...Using-Ops/examples/morphology/erode.ipynb → ...1-Using-ImageJ/Ops/morphology/erode.ipynb b/...Using-Ops/examples/morphology/erode.ipynb → ...1-Using-ImageJ/Ops/morphology/erode.ipynb
diff --git a/...ps/examples/morphology/extractHoles.ipynb → ...-ImageJ/Ops/morphology/extractHoles.ipynb b/...ps/examples/morphology/extractHoles.ipynb → ...-ImageJ/Ops/morphology/extractHoles.ipynb
diff --git a/...g-Ops/examples/morphology/fillHoles.ipynb → ...ing-ImageJ/Ops/morphology/fillHoles.ipynb b/...g-Ops/examples/morphology/fillHoles.ipynb → ...ing-ImageJ/Ops/morphology/fillHoles.ipynb
diff --git a/...g-Ops/examples/morphology/floodFill.ipynb → ...ing-ImageJ/Ops/morphology/floodFill.ipynb b/...g-Ops/examples/morphology/floodFill.ipynb → ...ing-ImageJ/Ops/morphology/floodFill.ipynb
diff --git a/...-Using-Ops/examples/morphology/open.ipynb → .../1-Using-ImageJ/Ops/morphology/open.ipynb b/...-Using-Ops/examples/morphology/open.ipynb → .../1-Using-ImageJ/Ops/morphology/open.ipynb
diff --git a/...ing-Ops/examples/morphology/outline.ipynb → ...Using-ImageJ/Ops/morphology/outline.ipynb b/...ing-Ops/examples/morphology/outline.ipynb → ...Using-ImageJ/Ops/morphology/outline.ipynb
diff --git a/...-Using-Ops/examples/morphology/thin.ipynb → .../1-Using-ImageJ/Ops/morphology/thin.ipynb b/...-Using-Ops/examples/morphology/thin.ipynb → .../1-Using-ImageJ/Ops/morphology/thin.ipynb
diff --git a/...sing-Ops/examples/morphology/topHat.ipynb → ...-Using-ImageJ/Ops/morphology/topHat.ipynb b/...sing-Ops/examples/morphology/topHat.ipynb → ...-Using-ImageJ/Ops/morphology/topHat.ipynb
diff --git a/...g-Ops/examples/segment/detectRidges.ipynb → ...ing-ImageJ/Ops/segment/detectRidges.ipynb b/...g-Ops/examples/segment/detectRidges.ipynb → ...ing-ImageJ/Ops/segment/detectRidges.ipynb
diff --git a/...s/4-Using-Ops/examples/segment/eval.ipynb → ...oks/1-Using-ImageJ/Ops/segment/eval.ipynb b/...s/4-Using-Ops/examples/segment/eval.ipynb → ...oks/1-Using-ImageJ/Ops/segment/eval.ipynb
diff --git a/...Using-Ops/examples/segment/identity.ipynb → ...1-Using-ImageJ/Ops/segment/identity.ipynb b/...Using-Ops/examples/segment/identity.ipynb → ...1-Using-ImageJ/Ops/segment/identity.ipynb
diff --git a/...ks/4-Using-Ops/examples/segment/map.ipynb → ...ooks/1-Using-ImageJ/Ops/segment/map.ipynb b/...ks/4-Using-Ops/examples/segment/map.ipynb → ...ooks/1-Using-ImageJ/Ops/segment/map.ipynb
diff --git a/.../4-Using-Ops/examples/segment/slice.ipynb → ...ks/1-Using-ImageJ/Ops/segment/slice.ipynb b/.../4-Using-Ops/examples/segment/slice.ipynb → ...ks/1-Using-ImageJ/Ops/segment/slice.ipynb
diff --git a/...ng-Ops/examples/stats/geometricMean.ipynb → ...sing-ImageJ/Ops/stats/geometricMean.ipynb b/...ng-Ops/examples/stats/geometricMean.ipynb → ...sing-ImageJ/Ops/stats/geometricMean.ipynb
diff --git a/...ing-Ops/examples/stats/harmonicMean.ipynb → ...Using-ImageJ/Ops/stats/harmonicMean.ipynb b/...ing-Ops/examples/stats/harmonicMean.ipynb → ...Using-ImageJ/Ops/stats/harmonicMean.ipynb
diff --git a/...sing-Ops/examples/stats/integralSum.ipynb → ...-Using-ImageJ/Ops/stats/integralSum.ipynb b/...sing-Ops/examples/stats/integralSum.ipynb → ...-Using-ImageJ/Ops/stats/integralSum.ipynb
diff --git a/...4-Using-Ops/examples/stats/kurtosis.ipynb → ...s/1-Using-ImageJ/Ops/stats/kurtosis.ipynb b/...4-Using-Ops/examples/stats/kurtosis.ipynb → ...s/1-Using-ImageJ/Ops/stats/kurtosis.ipynb
diff --git a/...ooks/4-Using-Ops/examples/stats/max.ipynb → notebooks/1-Using-ImageJ/Ops/stats/max.ipynb b/...ooks/4-Using-Ops/examples/stats/max.ipynb → notebooks/1-Using-ImageJ/Ops/stats/max.ipynb
diff --git a/...oks/4-Using-Ops/examples/stats/mean.ipynb → ...books/1-Using-ImageJ/Ops/stats/mean.ipynb b/...oks/4-Using-Ops/examples/stats/mean.ipynb → ...books/1-Using-ImageJ/Ops/stats/mean.ipynb
diff --git a/...s/4-Using-Ops/examples/stats/median.ipynb → ...oks/1-Using-ImageJ/Ops/stats/median.ipynb b/...s/4-Using-Ops/examples/stats/median.ipynb → ...oks/1-Using-ImageJ/Ops/stats/median.ipynb
diff --git a/...ooks/4-Using-Ops/examples/stats/min.ipynb → notebooks/1-Using-ImageJ/Ops/stats/min.ipynb b/...ooks/4-Using-Ops/examples/stats/min.ipynb → notebooks/1-Using-ImageJ/Ops/stats/min.ipynb
diff --git a/...s/4-Using-Ops/examples/stats/minMax.ipynb → ...oks/1-Using-ImageJ/Ops/stats/minMax.ipynb b/...s/4-Using-Ops/examples/stats/minMax.ipynb → ...oks/1-Using-ImageJ/Ops/stats/minMax.ipynb
diff --git a/...Ops/examples/stats/moment1AboutMean.ipynb → ...g-ImageJ/Ops/stats/moment1AboutMean.ipynb b/...Ops/examples/stats/moment1AboutMean.ipynb → ...g-ImageJ/Ops/stats/moment1AboutMean.ipynb
diff --git a/...Ops/examples/stats/moment2AboutMean.ipynb → ...g-ImageJ/Ops/stats/moment2AboutMean.ipynb b/...Ops/examples/stats/moment2AboutMean.ipynb → ...g-ImageJ/Ops/stats/moment2AboutMean.ipynb
diff --git a/...Ops/examples/stats/moment3AboutMean.ipynb → ...g-ImageJ/Ops/stats/moment3AboutMean.ipynb b/...Ops/examples/stats/moment3AboutMean.ipynb → ...g-ImageJ/Ops/stats/moment3AboutMean.ipynb
diff --git a/...Ops/examples/stats/moment4AboutMean.ipynb → ...g-ImageJ/Ops/stats/moment4AboutMean.ipynb b/...Ops/examples/stats/moment4AboutMean.ipynb → ...g-ImageJ/Ops/stats/moment4AboutMean.ipynb
diff --git a/...Using-Ops/examples/stats/percentile.ipynb → ...1-Using-ImageJ/Ops/stats/percentile.ipynb b/...Using-Ops/examples/stats/percentile.ipynb → ...1-Using-ImageJ/Ops/stats/percentile.ipynb
diff --git a/...4-Using-Ops/examples/stats/quantile.ipynb → ...s/1-Using-ImageJ/Ops/stats/quantile.ipynb b/...4-Using-Ops/examples/stats/quantile.ipynb → ...s/1-Using-ImageJ/Ops/stats/quantile.ipynb
diff --git a/...oks/4-Using-Ops/examples/stats/size.ipynb → ...books/1-Using-ImageJ/Ops/stats/size.ipynb b/...oks/4-Using-Ops/examples/stats/size.ipynb → ...books/1-Using-ImageJ/Ops/stats/size.ipynb
diff --git a/...4-Using-Ops/examples/stats/skewness.ipynb → ...s/1-Using-ImageJ/Ops/stats/skewness.ipynb b/...4-Using-Ops/examples/stats/skewness.ipynb → ...s/1-Using-ImageJ/Ops/stats/skewness.ipynb
diff --git a/...s/4-Using-Ops/examples/stats/stdDev.ipynb → ...oks/1-Using-ImageJ/Ops/stats/stdDev.ipynb b/...s/4-Using-Ops/examples/stats/stdDev.ipynb → ...oks/1-Using-ImageJ/Ops/stats/stdDev.ipynb
diff --git a/...ooks/4-Using-Ops/examples/stats/sum.ipynb → notebooks/1-Using-ImageJ/Ops/stats/sum.ipynb b/...ooks/4-Using-Ops/examples/stats/sum.ipynb → notebooks/1-Using-ImageJ/Ops/stats/sum.ipynb
diff --git a/...ng-Ops/examples/stats/sumOfInverses.ipynb → ...sing-ImageJ/Ops/stats/sumOfInverses.ipynb b/...ng-Ops/examples/stats/sumOfInverses.ipynb → ...sing-ImageJ/Ops/stats/sumOfInverses.ipynb
diff --git a/...-Using-Ops/examples/stats/sumOfLogs.ipynb → .../1-Using-ImageJ/Ops/stats/sumOfLogs.ipynb b/...-Using-Ops/examples/stats/sumOfLogs.ipynb → .../1-Using-ImageJ/Ops/stats/sumOfLogs.ipynb
diff --git a/...ing-Ops/examples/stats/sumOfSquares.ipynb → ...Using-ImageJ/Ops/stats/sumOfSquares.ipynb b/...ing-Ops/examples/stats/sumOfSquares.ipynb → ...Using-ImageJ/Ops/stats/sumOfSquares.ipynb
diff --git a/...4-Using-Ops/examples/stats/variance.ipynb → ...s/1-Using-ImageJ/Ops/stats/variance.ipynb b/...4-Using-Ops/examples/stats/variance.ipynb → ...s/1-Using-ImageJ/Ops/stats/variance.ipynb
diff --git a/...ng-Ops/examples/threshold/threshold.ipynb → ...sing-ImageJ/Ops/threshold/threshold.ipynb b/...ng-Ops/examples/threshold/threshold.ipynb → ...sing-ImageJ/Ops/threshold/threshold.ipynb
diff --git a/...examples/transform/addDimensionView.ipynb → ...ageJ/Ops/transform/addDimensionView.ipynb b/...examples/transform/addDimensionView.ipynb → ...ageJ/Ops/transform/addDimensionView.ipynb
diff --git a/.../examples/transform/concatenateView.ipynb → ...mageJ/Ops/transform/concatenateView.ipynb b/.../examples/transform/concatenateView.ipynb → ...mageJ/Ops/transform/concatenateView.ipynb
diff --git a/...4-Using-Ops/examples/transform/crop.ipynb → ...s/1-Using-ImageJ/Ops/transform/crop.ipynb b/...4-Using-Ops/examples/transform/crop.ipynb → ...s/1-Using-ImageJ/Ops/transform/crop.ipynb
diff --git a/...ansform/dropSingletonDimensionsView.ipynb → ...ansform/dropSingletonDimensionsView.ipynb b/...ansform/dropSingletonDimensionsView.ipynb → ...ansform/dropSingletonDimensionsView.ipynb
diff --git a/...examples/transform/extendBorderView.ipynb → ...ageJ/Ops/transform/extendBorderView.ipynb b/...examples/transform/extendBorderView.ipynb → ...ageJ/Ops/transform/extendBorderView.ipynb
diff --git a/...es/transform/extendMirrorDoubleView.ipynb → ...ps/transform/extendMirrorDoubleView.ipynb b/...es/transform/extendMirrorDoubleView.ipynb → ...ps/transform/extendMirrorDoubleView.ipynb
diff --git a/...es/transform/extendMirrorSingleView.ipynb → ...ps/transform/extendMirrorSingleView.ipynb b/...es/transform/extendMirrorSingleView.ipynb → ...ps/transform/extendMirrorSingleView.ipynb
diff --git a/...amples/transform/extendPeriodicView.ipynb → ...eJ/Ops/transform/extendPeriodicView.ipynb b/...amples/transform/extendPeriodicView.ipynb → ...eJ/Ops/transform/extendPeriodicView.ipynb
diff --git a/...examples/transform/extendRandomView.ipynb → ...ageJ/Ops/transform/extendRandomView.ipynb b/...examples/transform/extendRandomView.ipynb → ...ageJ/Ops/transform/extendRandomView.ipynb
diff --git a/.../examples/transform/extendValueView.ipynb → ...mageJ/Ops/transform/extendValueView.ipynb b/.../examples/transform/extendValueView.ipynb → ...mageJ/Ops/transform/extendValueView.ipynb
diff --git a/...g-Ops/examples/transform/extendView.ipynb → ...ing-ImageJ/Ops/transform/extendView.ipynb b/...g-Ops/examples/transform/extendView.ipynb → ...ing-ImageJ/Ops/transform/extendView.ipynb
diff --git a/...s/examples/transform/extendZeroView.ipynb → ...ImageJ/Ops/transform/extendZeroView.ipynb b/...s/examples/transform/extendZeroView.ipynb → ...ImageJ/Ops/transform/extendZeroView.ipynb
diff --git a/...examples/transform/flatIterableView.ipynb → ...ageJ/Ops/transform/flatIterableView.ipynb b/...examples/transform/flatIterableView.ipynb → ...ageJ/Ops/transform/flatIterableView.ipynb
diff --git a/...s/examples/transform/hyperSliceView.ipynb → ...ImageJ/Ops/transform/hyperSliceView.ipynb b/...s/examples/transform/hyperSliceView.ipynb → ...ImageJ/Ops/transform/hyperSliceView.ipynb
diff --git a/.../examples/transform/interpolateView.ipynb → ...mageJ/Ops/transform/interpolateView.ipynb b/.../examples/transform/interpolateView.ipynb → ...mageJ/Ops/transform/interpolateView.ipynb
diff --git a/...Ops/examples/transform/intervalView.ipynb → ...g-ImageJ/Ops/transform/intervalView.ipynb b/...Ops/examples/transform/intervalView.ipynb → ...g-ImageJ/Ops/transform/intervalView.ipynb
diff --git a/...s/examples/transform/invertAxisView.ipynb → ...ImageJ/Ops/transform/invertAxisView.ipynb b/...s/examples/transform/invertAxisView.ipynb → ...ImageJ/Ops/transform/invertAxisView.ipynb
diff --git a/...g-Ops/examples/transform/offsetView.ipynb → ...ing-ImageJ/Ops/transform/offsetView.ipynb b/...g-Ops/examples/transform/offsetView.ipynb → ...ing-ImageJ/Ops/transform/offsetView.ipynb
diff --git a/...sform/permuteCoordinatesInverseView.ipynb → ...sform/permuteCoordinatesInverseView.ipynb b/...sform/permuteCoordinatesInverseView.ipynb → ...sform/permuteCoordinatesInverseView.ipynb
diff --git a/...es/transform/permuteCoordinatesView.ipynb → ...ps/transform/permuteCoordinatesView.ipynb b/...es/transform/permuteCoordinatesView.ipynb → ...ps/transform/permuteCoordinatesView.ipynb
diff --git a/...-Ops/examples/transform/permuteView.ipynb → ...ng-ImageJ/Ops/transform/permuteView.ipynb b/...-Ops/examples/transform/permuteView.ipynb → ...ng-ImageJ/Ops/transform/permuteView.ipynb
diff --git a/...sing-Ops/examples/transform/project.ipynb → ...-Using-ImageJ/Ops/transform/project.ipynb b/...sing-Ops/examples/transform/project.ipynb → ...-Using-ImageJ/Ops/transform/project.ipynb
diff --git a/...g-Ops/examples/transform/rotateView.ipynb → ...ing-ImageJ/Ops/transform/rotateView.ipynb b/...g-Ops/examples/transform/rotateView.ipynb → ...ing-ImageJ/Ops/transform/rotateView.ipynb
diff --git a/...ng-Ops/examples/transform/scaleView.ipynb → ...sing-ImageJ/Ops/transform/scaleView.ipynb b/...ng-Ops/examples/transform/scaleView.ipynb → ...sing-ImageJ/Ops/transform/scaleView.ipynb
diff --git a/...ng-Ops/examples/transform/shearView.ipynb → ...sing-ImageJ/Ops/transform/shearView.ipynb b/...ng-Ops/examples/transform/shearView.ipynb → ...sing-ImageJ/Ops/transform/shearView.ipynb
diff --git a/...ng-Ops/examples/transform/stackView.ipynb → ...sing-ImageJ/Ops/transform/stackView.ipynb b/...ng-Ops/examples/transform/stackView.ipynb → ...sing-ImageJ/Ops/transform/stackView.ipynb
diff --git a/...ps/examples/transform/subsampleView.ipynb → ...-ImageJ/Ops/transform/subsampleView.ipynb b/...ps/examples/transform/subsampleView.ipynb → ...-ImageJ/Ops/transform/subsampleView.ipynb
diff --git a/...ps/examples/transform/translateView.ipynb → ...-ImageJ/Ops/transform/translateView.ipynb b/...ps/examples/transform/translateView.ipynb → ...-ImageJ/Ops/transform/translateView.ipynb
diff --git a/...-Ops/examples/transform/unshearView.ipynb → ...ng-ImageJ/Ops/transform/unshearView.ipynb b/...-Ops/examples/transform/unshearView.ipynb → ...ng-ImageJ/Ops/transform/unshearView.ipynb
diff --git a/...-Ops/examples/transform/zeroMinView.ipynb → ...ng-ImageJ/Ops/transform/zeroMinView.ipynb b/...-Ops/examples/transform/zeroMinView.ipynb → ...ng-ImageJ/Ops/transform/zeroMinView.ipynb
diff --git a/...ooks/2-ImageJ-Basics/ide-autocomplete.png → ...books/1-Using-ImageJ/ide-autocomplete.png b/...ooks/2-ImageJ-Basics/ide-autocomplete.png → ...books/1-Using-ImageJ/ide-autocomplete.png
diff --git a/...s/3-Extending-ImageJ/2-Input-Output.ipynb → ...s/2-Extending-ImageJ/1-Input-Output.ipynb b/...s/3-Extending-ImageJ/2-Input-Output.ipynb → ...s/2-Extending-ImageJ/1-Input-Output.ipynb
@@ -459,7 +459,7 @@
    "mimetype": "",
    "name": "Groovy",
    "nbconverter_exporter": "",
-   "version": "2.4.3"
+   "version": "2.5.6"
   },
   "toc": {
    "base_numbering": 1,

diff --git a/notebooks/4-Using-Ops/4-Ops.ipynb → notebooks/2-Extending-ImageJ/2-Ops.ipynb b/notebooks/4-Using-Ops/4-Ops.ipynb → notebooks/2-Extending-ImageJ/2-Ops.ipynb
@@ -479,7 +479,7 @@
    "mimetype": "",
    "name": "Groovy",
    "nbconverter_exporter": "",
-   "version": "2.4.3"
+   "version": "2.5.6"
   },
   "toc": {
    "base_numbering": 1,

diff --git a/...-Core-Libraries/1-SciJava-in-Detail.ipynb → ...Advanced-Topics/1-SciJava-in-Detail.ipynb b/...-Core-Libraries/1-SciJava-in-Detail.ipynb → ...Advanced-Topics/1-SciJava-in-Detail.ipynb
diff --git a/...-Core-Libraries/2-ImgLib2-in-Detail.ipynb → ...Advanced-Topics/2-ImgLib2-in-Detail.ipynb b/...-Core-Libraries/2-ImgLib2-in-Detail.ipynb → ...Advanced-Topics/2-ImgLib2-in-Detail.ipynb
diff --git a/...-Core-Libraries/3-Using-Special-Ops.ipynb → ...Advanced-Topics/3-Using-Special-Ops.ipynb b/...-Core-Libraries/3-Using-Special-Ops.ipynb → ...Advanced-Topics/3-Using-Special-Ops.ipynb
diff --git a/notebooks/3-Extending-ImageJ/3-Commands.ipynb b/notebooks/3-Extending-ImageJ/3-Commands.ipynb
diff --git a/notebooks/3-Extending-ImageJ/5-Tools.ipynb b/notebooks/3-Extending-ImageJ/5-Tools.ipynb
diff --git a/notebooks/ImageJ-Tutorials-and-Demo.ipynb b/notebooks/ImageJ-Tutorials-and-Demo.ipynb
@@ -40,33 +40,20 @@
     "      <li><a href=\"1-Using-ImageJ/4-Tables.ipynb\">Tables</a></li>\n",
     "      <li><a href=\"1-Using-ImageJ/5-Mixed-World-ImageJ1.ipynb\">Mixed World: Using ImageJ 1.x</a></li>\n",
     "      <li><a href=\"1-Using-ImageJ/6-ImageJ-with-Python-Kernel.ipynb\">ImageJ with Python Kernel</a></li>\n",
+    "      <li><a href=\"1-Using-ImageJ/7-Calling-Scripts-from-Scripts.ipynb\">Calling Scripts from Scripts</a></li>\n",
     "    </ol>\n",
     "  </div>\n",
-    "  <div class=\"col-md-5\">\n",
-    "    <h2>Extending ImageJ</h2>\n",
-    "    <ol>\n",
-    "      <li><a href=\"2-Extending-ImageJ/1-Scripting.ipynb\">Scripting: the easy way to extend ImageJ</a> (incomplete)</li>\n",
-    "      <li><a href=\"2-Extending-ImageJ/2-Input-Output.ipynb\">Extending ImageJ: Data Input and Output</a></li>\n",
-    "      <li><a href=\"2-Extending-ImageJ/3-Commands.ipynb\">Extending ImageJ: Commands</a> (placeholder)</li>\n",
-    "      <li><a href=\"2-Extending-ImageJ/4-Ops.ipynb\">Extending ImageJ: Ops</a></li>\n",
-    "      <li><a href=\"2-Extending-ImageJ/5-Tools.ipynb\">Extending ImageJ: Tools</a> (placeholder)</li>\n",
-    "    </ol>\n",
-    "  </div>\n",
-    "</div>\n",
-    "<div class=\"row\">\n",
     "  <div class=\"col-md-6\">\n",
-    "    <h2>Advanced usage</h2>\n",
+    "    <h2>Extending ImageJ</h2>\n",
     "    <ol>\n",
-    "      <li><a href=\"3-Advanced-Usage/1-SciJava-in-Detail.ipynb\">SciJava in Detail</a></li>\n",
-    "      <li><a href=\"3-Advanced-Usage/2-ImgLib2-in-Detail.ipynb\">ImgLib2 in Detail</a></li>\n",
+    "      <li><a href=\"2-Extending-ImageJ/1-Input-Output.ipynb\">IOPlugins - Data Input and Output</a></li>\n",
+    "      <li><a href=\"2-Extending-ImageJ/2-Ops.ipynb\">Ops - Image Algorithms</a></li>\n",
     "    </ol>\n",
-    "  </div>\n",
-    "  <div class=\"col-md-5\">\n",
-    "    <h2>Advanced extensions</h2>\n",
+    "    <h2>Advanced Topics</h2>\n",
     "    <ol>\n",
-    "      <li>Creating a custom service (coming later)</li>\n",
-    "      <li>Customizing module execution (coming later)</li>\n",
-    "      <li>Creating a SCIFIO plugin (coming later)</li>\n",
+    "      <li><a href=\"3-Advanced-Topics/1-SciJava-in-Detail.ipynb\">SciJava in Detail</a></li>\n",
+    "      <li><a href=\"3-Advanced-Topics/2-ImgLib2-in-Detail.ipynb\">ImgLib2 in Detail</a></li>\n",
+    "      <li><a href=\"3-Advanced-Topics/3-Using-Special-Ops.ipynb\">Using Special Ops</a></li>\n",
     "    </ol>\n",
     "  </div>\n",
     "</div>\n",
@@ -119,7 +106,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a2c0421d-1742-4555-ad30-4efc31cae762",
+       "model_id": "95ac493c-41e0-4cfb-8108-4817ef4fe78b",
        "version_major": 2,
        "version_minor": 0
       },
@@ -252,7 +239,6 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[INFO] Populating metadata\n",
       "[INFO] Populating metadata\n"
      ]
     },