Merge pull request #23 from pwalczysko/notebook-text

Modify text of the idr0062... notebook

notebooks/idr0062_pixel_classification_zarr.ipynb

@@ -4,16 +4,16 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Analyze Zarr Image from a public S3 repository using ilastik \n",
-    "The notebook shows how to load an IDR image converted into a Zarr file.\n",
+    "# Load Zarr Image with labels from a public S3 repository, analyze using ilastik and compare results.\n",
+    "The notebook shows how to load an IDR image converted into a Zarr file with labels.\n",
     "\n",
-    "The image is then analyzed using [ilastik](https://ilastik.github.io/).\n",
-    "The image is taken from  the paper \"NesSys: a novel method for accurate nuclear segmentation in 3D\" published August 2019 in PLOS Biology: https://doi.org/10.1371/journal.pbio.3000388\n",
+    "The image is referenced in the paper \"NesSys: a novel method for accurate nuclear segmentation in 3D\" published August 2019 in PLOS Biology: https://doi.org/10.1371/journal.pbio.3000388 and can be viewed online in the [Image Data Resource](https://idr.openmicroscopy.org/webclient/?show=image-6001247).\n",
     "\n",
-    "The images can be viewed online in the [Image Data Resource](https://idr.openmicroscopy.org/webclient/?show=project-801).\n",
+    "This original image was converted into the Zarr format. The analysis results produced by the paper authors were converted into labels and linked to the Zarr file which was placed into a public S3 repository.\n",
     "\n",
-    "Binary data are read from a public S3 repository.\n",
-    "The dimension might need to be adjusted depending on the ilastik project."
+    "In this notebook, the converted Zarr file is then loaded together with the labels from the S3 storage and analyzed using [ilastik](https://ilastik.github.io/). The ilastik analysis produces a probability map based on pixel classification. These probability maps are then viewed side-by-side with the original segmentations produced by the authors of the papers obtained via the loaded labels.\n",
+    "\n",
+    "If you run this notebook with different images or ilastik projects, the dimension might need to be adjusted depending on the ilastik project."
    ]
   },
   {
@@ -154,7 +154,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Store the channels data so we can compare them with the results of the pixel classification later."
+    "### Store the original image channels for later comparison with probability map generated by ilastik."
    ]
   },
   {
@@ -171,7 +171,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Load each image as a 5D-numpy array and analyze."
+    "### Load each image as a 5D-numpy array and analyze in ilastik."
    ]
   },
   {
@@ -293,7 +293,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### View the first channel and the analysis result side-by-side"
+    "###  Compare raw data with the ilastik result.\n",
+    "View the first channel of the original image (left) and the probability map created by pixel classification module of ilastik (right) side-by-side."
    ]
   },
   {
@@ -326,9 +327,11 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Compare the labels and the analysis output\n",
-    "The first 2 planes do not have labels.\n",
-    "On the left, the labels saved in S3. On the rigth, the analysis results."
+    "### Compare the original analysis result with the ilastik result.\n",
+    "\n",
+    "On the left, the labels loaded from S3 representing the original analysis by the authors of the paper. On the rigth, the probability maps from the pixel classification module of ilastik.\n",
+    "\n",
+    "The first 2 z-planes do not have labels."
    ]
   },
   {
@@ -359,7 +362,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Combine the  pixels classification map and the labels."
+    "### Overlay the original analysis result and the ilastik result."
    ]
   },
   {