Improve tutorials according to PR #57

The tutorials moved on a lot since that PR, so I had to redo the patch.
I tried to incorporate everything that was still relevant.

Co-authored-by: David Kolb <[email protected]>
Co-authored-by: Gabriel Selzer <[email protected]>
Co-authored-by: Jan Eglinger <[email protected]>

Closes #57.

Author: ctrueden

notebooks/1-Using-ImageJ/1-Fundamentals.ipynb

@@ -191,7 +191,7 @@
     "\n",
     "<p><img src=\"ide-autocomplete.png\"></p>\n",
     "\n",
-    "Unfortunately, here in this notebook software, the autocompletion logic is not (yet!) advanced enough to fully offer such a feature—there is only rudimentary method completion support by pressing <kbd>tab</kbd>. Hence, the `NotebookService` also includes a handy method for inspecting an object's methods. Here is an example:"
+    "Unfortunately, here in this notebook software, the autocompletion logic is not (yet!) advanced enough to fully offer such a feature—there is only rudimentary method completion support by pressing <kbd>tab</kbd>. Hence, the `NotebookService` also includes a handy method for inspecting an object's methods. Here is an example which will show the available methods of a List:"
    ]
   },
   {
@@ -456,7 +456,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "A SciJava _module_ in an executable snippet of code with _typed inputs and outputs_. You can think of them as <a href=\"https://en.wikipedia.org/wiki/Subroutine\">subroutines</a>, also called _functions_ or _methods_ depending on the programming language.\n",
+    "A SciJava _module_ is an executable snippet of code with _typed inputs and outputs_. You can think of them as <a href=\"https://en.wikipedia.org/wiki/Subroutine\">subroutines</a>, also called _functions_ or _methods_ depending on the programming language.\n",
     "\n",
     "The two most common flavors of module are _commands_ and _scripts_. A `Command` is a plugin written in Java, whereas a script is written in one of the many available [SciJava scripting languages](https://imagej.net/Scripting). Most users who need to code a module will use a script, because they are simpler to write."
    ]
@@ -690,7 +690,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The true meat of ImageJ is [ImageJ Ops](https://imagej.net/Ops), a library for reusable image processing. An `Op` plugin is form of `Command`, and therefore a module.\n",
+    "The true meat of ImageJ is [ImageJ Ops](https://imagej.net/Ops), a library for reusable image processing. An `Op` plugin is a form of `Command`, and therefore a module.\n",
     "\n",
     "Please proceed to the [ImageJ Ops](2-ImageJ-Ops.ipynb) tutorial notebook for a primer with lots of examples!"
    ]

notebooks/1-Using-ImageJ/2-ImageJ-Ops.ipynb

@@ -564,7 +564,8 @@
    "source": [
     "The `equation` op allows you to generate an image from a formula in JavaScript syntax.\n",
     "\n",
-    "Such images can be useful for testing without needing an external image source, or a long and bulky list of numbers."
+    "Such images can be useful for testing without needing an external image source, or a long and bulky list of numbers.\n",
+    "This `Op` will execute the equation on each pixel of the image. Within the equation the current location can be retrieved via the variable `p[]` (see example equation below)."
    ]
   },
   {
@@ -984,7 +985,7 @@
    "source": [
     "You can also call any op in an `eval` statement as a function, using familiar function syntax.\n",
     "\n",
-    "Here is an example of the `eval` op being used to compute a [Difference of Gaussians](https://en.wikipedia.org/wiki/Difference_of_Gaussians):"
+    "The following is an example of the `eval` op being used to compute a [Difference of Gaussians](https://en.wikipedia.org/wiki/Difference_of_Gaussians). Inputs within the formula may be accessed via the `Map vars?` argument of the eval function and the key of the map corresponds to the name of the variable that can be used in the formula."
    ]
   },
   {
@@ -1579,7 +1580,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Convolution is a very helpful filter for many circumstances. Below is an example of how to use the convolution filter. "
+    "[Convolution](https://en.wikipedia.org/wiki/Convolution) is a very helpful filter for many circumstances. Below is an example of how to use the convolution filter."
    ]
   },
   {
@@ -2059,6 +2060,14 @@
    "execution_count": 49,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Eye bounds: (0, 0) - (39, 27)\n",
+      "EyeView bounds: (75, 27) - (114, 54)\n"
+     ]
+    },
     {
      "data": {
       "text/html": [
@@ -2077,6 +2086,8 @@
     "eye = ij.op().run(\"crop\", image, region)\n",
     "eyeView = ij.op().run(\"intervalView\", image, region)\n",
     "\n",
+    "println(\"Eye bounds: \" + bounds(eye))\n",
+    "println(\"EyeView bounds: \" + bounds(eyeView))\n",
     "ij.notebook().display([[\"eye\":eye, \"view\":eyeView]])"
    ]
   },
@@ -2543,8 +2554,8 @@
    "source": [
     "Ops includes operators for mathematical morphology in both binary and grayscale. The two most basic morphological operators are:\n",
     "\n",
-    "* erosion – reducing bright pixels at the borders\n",
-    "* dilation - growing bright pixels at the borders\n",
+    "* erosion – reducing bright pixels at the edges of the image\n",
+    "* dilation - growing bright pixels at the edges of the image\n",
     "\n",
     "The next two most basic are:\n",
     "\n",