remove some comments

README.md

@@ -176,7 +176,7 @@ import matplotlib.pyplot as plt
 
 root = copick.from_croissant(
     "https://huggingface.co/datasets/uermel/popsicle/resolve/main/phantom/Croissant/metadata.json",
-    overlay_root="/tmp/popsicle-overlay",  # forces Mode B (read-only manifest)
+    overlay_root="/tmp/popsicle-overlay",  
     static_fs_args={"anon": True},          # public portal bucket
 )
 
@@ -258,7 +258,7 @@ import matplotlib.pyplot as plt
 
 root = copick.from_croissant(
     "https://huggingface.co/datasets/uermel/popsicle/resolve/main/bacterial/Croissant/metadata.json",
-    overlay_root="/tmp/popsicle-overlay",  # forces Mode B (read-only manifest)
+    overlay_root="/tmp/popsicle-overlay",  
     static_fs_args={"anon": True},          # public portal bucket
 )
 
@@ -281,8 +281,6 @@ ax.imshow(arr[z_mid], cmap="gray")
 cmap = plt.get_cmap("tab10")
 for i, seg in enumerate(run.segmentations):
     mask = seg.numpy()[z_mid]            # (Y, X) — same shape as the tomo slice
-    # Replace the binary 1s with i so each class maps to a different tab10 index;
-    # otherwise every overlay renders as tab10[1].
     layer = np.ma.masked_where(mask == 0, np.full_like(mask, i, dtype=np.int8))
     ax.imshow(layer, cmap=cmap, vmin=0, vmax=10, alpha=0.4, interpolation="none")
     # one-line legend hack: scatter a single point off-image with the class color
@@ -347,7 +345,7 @@ import matplotlib.pyplot as plt
 
 root = copick.from_croissant(
     "https://huggingface.co/datasets/uermel/popsicle/resolve/main/yeast/Croissant/metadata.json",
-    overlay_root="/tmp/popsicle-overlay",  # forces Mode B (read-only manifest)
+    overlay_root="/tmp/popsicle-overlay", 
     static_fs_args={"anon": True},          # public portal bucket
 )
 
@@ -424,7 +422,7 @@ import matplotlib.pyplot as plt
 
 root = copick.from_croissant(
     "https://huggingface.co/datasets/uermel/popsicle/resolve/main/motorbench/Croissant/metadata.json",
-    overlay_root="/tmp/popsicle-overlay",  # forces Mode B (read-only manifest)
+    overlay_root="/tmp/popsicle-overlay",  
     static_fs_args={"anon": True},          # public portal bucket
 )
 
@@ -434,9 +432,7 @@ for split, run_names in root.splits.items():
     print(f"{split}: {len(run_names)} runs ({len(runs_with)} with motor picks)")
 
 # Visualize: midplane slice of one *V. cholerae* test tomogram with motor
-# centers overlaid as crosses. Copick's CDP backend uses the portal Run.id
-# as run.name — sma2022-08-05-19 -> Run.id 33914 -> copick run.name "33914".
-# The portal Run.name is preserved on `run.portal_run_name` for round-tripping.
+# centers overlaid as crosses. 
 run = root.get_run("33914")
 vs = run.voxel_spacings[0]
 tomo = vs.tomograms[0]

demos.ipynb

@@ -72,7 +72,7 @@
     "\n",
     "root = copick.from_croissant(\n",
     "    PHANTOM_URL,\n",
-    "    overlay_root=\"/tmp/popsicle-overlay\",  # forces Mode B (read-only manifest)\n",
+    "    overlay_root=\"/tmp/popsicle-overlay\",\n",
     "    static_fs_args={\"anon\": True},          # public portal bucket\n",
     ")\n",
     "\n",
@@ -145,7 +145,7 @@
     "\n",
     "root = copick.from_croissant(\n",
     "    BACTERIAL_URL,\n",
-    "    overlay_root=\"/tmp/popsicle-overlay\",  # forces Mode B (read-only manifest)\n",
+    "    overlay_root=\"/tmp/popsicle-overlay\",\n",
     "    static_fs_args={\"anon\": True},          # public portal bucket\n",
     ")\n",
     "\n",
@@ -177,8 +177,6 @@
     "cmap = plt.get_cmap(\"tab10\")\n",
     "for i, seg in enumerate(run.segmentations):\n",
     "    mask = seg.numpy()[z_mid]            # (Y, X) — same shape as the tomo slice\n",
-    "    # Substitute the binary mask values with i so each class maps to a\n",
-    "    # different tab10 index (otherwise every overlay renders as tab10[1]).\n",
     "    layer = np.ma.masked_where(mask == 0, np.full_like(mask, i, dtype=np.int8))\n",
     "    ax.imshow(layer, cmap=cmap, vmin=0, vmax=10, alpha=0.4, interpolation=\"none\")\n",
     "    ax.scatter([], [], color=cmap(i), label=seg.name)\n",
@@ -211,7 +209,7 @@
     "\n",
     "root = copick.from_croissant(\n",
     "    YEAST_URL,\n",
-    "    overlay_root=\"/tmp/popsicle-overlay\",  # forces Mode B (read-only manifest)\n",
+    "    overlay_root=\"/tmp/popsicle-overlay\",\n",
     "    static_fs_args={\"anon\": True},          # public portal bucket\n",
     ")\n",
     "\n",
@@ -282,7 +280,7 @@
     "\n",
     "root = copick.from_croissant(\n",
     "    MOTORBENCH_URL,\n",
-    "    overlay_root=\"/tmp/popsicle-overlay\",  # forces Mode B (read-only manifest)\n",
+    "    overlay_root=\"/tmp/popsicle-overlay\",\n",
     "    static_fs_args={\"anon\": True},          # public portal bucket\n",
     ")\n",
     "\n",