Add standalone mask examples on black backgrounds

README.md

@@ -169,6 +169,45 @@ plt.show()
 
 Each row shows the colour image and its marked nuclei.
 
+Two examples without the image underneath. Black marks background; bright instance colours distinguish objects, not cell types. Class colours match the overlay examples above.
+
+```python
+from skimage.color import label2rgb
+
+instance_colors = [
+    (1, 0.85, 0.2),
+    (0.2, 1, 1),
+    (1, 0.3, 0.8),
+    (0.5, 1, 0.2),
+    (0.65, 0.55, 1),
+]
+mask_samples = samples.to_dicts()
+mask_samples = [mask_samples[0], mask_samples[-1]]
+mask_layers = [("inst", "Nucleus instances"), ("type", "Nucleus classes")]
+mask_fig, mask_axes = plt.subplots(2, 2, figsize=(6.4, 8))
+for row_axes, sample in zip(mask_axes, mask_samples):
+    for column, (ax, (key, title)) in enumerate(zip(row_axes, mask_layers)):
+        labels = read_png(sample[key])
+        if key == "type":
+            pixels = nucleus_colors[labels]
+        else:
+            pixels = label2rgb(
+                labels, colors=instance_colors, bg_label=0, bg_color=(0, 0, 0)
+            )
+        ax.imshow(pixels, interpolation="nearest")
+        ax.set_axis_off()
+    label = sample["id"]
+    row_axes[0].text(0, 1.02, label, transform=row_axes[0].transAxes, fontsize=8)
+for ax, (_, title) in zip(mask_axes[0], mask_layers):
+    ax.set_title(title, fontsize=10, pad=18)
+mask_fig.subplots_adjust(
+    left=0.01, right=0.99, bottom=0.02, top=0.94, hspace=0.16, wspace=0.03
+)
+plt.show()
+```
+
+![Two examples of the annotation masks without image backgrounds](masks.png)
+
 ## Preparation and validation
 
 The [original PanNuke masks](https://warwick.ac.uk/fac/cross_fac/tia/data/pannuke/) store each cell class separately. These were combined into `inst` and `type`, keeping every nucleus and assigning new nucleus numbers within each image. Where source masks overlap, the lower class number wins. Image size and colour values are unchanged.

manifest.json

@@ -136,12 +136,16 @@
   ],
   "documentation": {
     "README.md": {
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+      "sha256": "0a3cab01cdf4c42212239be4bbb6b0314b0702ab6b7a74377e39418b85817580",
+      "bytes": 7708
     },
     "examples.png": {
       "sha256": "d281d4048618bcb91a1b8d919c70638f28778f8267b4d1e5ff98f914159a7cb2",
       "bytes": 394767
+    },
+    "masks.png": {
+      "sha256": "4ca487b5e39d90d957761bd013c711760be5e0882a297bb4339f49c7eda8b3da",
+      "bytes": 31208
     }
   }
 }