addditional cell images

benchmark/12.visualize-brd4.ipynb

@@ -67,7 +67,7 @@
     "        ).folder_name.values[0]\n",
     "        row_name = f\"r{row.row}\"\n",
     "        col_name = f\"c{row.col}\"\n",
-    "        if row.Number_of_images > 30000: # hack for identifying wells with 16 fields of view.\n",
+    "        if row.Number_of_images > 30000 or (perturbation==\"crispr\" and row.gene==\"PLK1\"): # hack for identifying wells with 16 fields of view.\n",
     "            field = f\"f08\"\n",
     "        else:\n",
     "            field = f\"f05\"\n",
@@ -169,7 +169,7 @@
     "    \"../metadata/external_metadata/JUMP-Target-1_orf_metadata.tsv\",\n",
     "    sep=\"\\t\",\n",
     "    usecols=[\"broad_sample\", \"gene\", \"control_type\"],\n",
-    ").query('gene == \"BRD4\" or control_type==\"negcon\"')\n",
+    ").query('gene == \"BRD4\" or gene == \"PLK1\" or control_type==\"negcon\"')\n",
     "\n",
     "# Select one random CRISPR control treatment\n",
     "\n",
@@ -336,7 +336,58 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|██████████| 18/18 [00:00<00:00, 1209.49it/s]\n"
+      "  0%|          | 0/20 [00:00<?, ?it/s]"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "download: s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117006__2020-11-02T19_54_45-Measurement1/Images/r14c08f05p01-ch1sk1fk1fl1.tiff to figures/BRD4/A549/orf/PLK1/r14c08f05p01-ch1sk1fk1fl1.tiff\n",
+      "download: s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117006__2020-11-02T19_54_45-Measurement1/Images/r14c08f05p01-ch2sk1fk1fl1.tiff to figures/BRD4/A549/orf/PLK1/r14c08f05p01-ch2sk1fk1fl1.tiff\n",
+      "download: s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117006__2020-11-02T19_54_45-Measurement1/Images/r14c08f05p01-ch3sk1fk1fl1.tiff to figures/BRD4/A549/orf/PLK1/r14c08f05p01-ch3sk1fk1fl1.tiff\n",
+      "download: s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117006__2020-11-02T19_54_45-Measurement1/Images/r14c08f05p01-ch4sk1fk1fl1.tiff to figures/BRD4/A549/orf/PLK1/r14c08f05p01-ch4sk1fk1fl1.tiff\n",
+      "Completed 1.5 MiB/2.1 MiB (821.4 KiB/s) with 1 file(s) remaining                     \r"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      " 80%|████████  | 16/20 [01:03<00:15,  3.95s/it]"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "download: s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117006__2020-11-02T19_54_45-Measurement1/Images/r14c08f05p01-ch5sk1fk1fl1.tiff to figures/BRD4/A549/orf/PLK1/r14c08f05p01-ch5sk1fk1fl1.tiff\n",
+      "download: s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00118039__2020-11-02T18_16_01-Measurement1/Images/r14c08f05p01-ch1sk1fk1fl1.tiff to figures/BRD4/U2OS/orf/PLK1/r14c08f05p01-ch1sk1fk1fl1.tiff\n",
+      "download: s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00118039__2020-11-02T18_16_01-Measurement1/Images/r14c08f05p01-ch2sk1fk1fl1.tiff to figures/BRD4/U2OS/orf/PLK1/r14c08f05p01-ch2sk1fk1fl1.tiff\n",
+      "download: s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00118039__2020-11-02T18_16_01-Measurement1/Images/r14c08f05p01-ch3sk1fk1fl1.tiff to figures/BRD4/U2OS/orf/PLK1/r14c08f05p01-ch3sk1fk1fl1.tiff\n",
+      "download: s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00118039__2020-11-02T18_16_01-Measurement1/Images/r14c08f05p01-ch4sk1fk1fl1.tiff to figures/BRD4/U2OS/orf/PLK1/r14c08f05p01-ch4sk1fk1fl1.tiff\n",
+      "Completed 1.8 MiB/2.1 MiB (901.7 KiB/s) with 1 file(s) remaining                     \r"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "100%|██████████| 20/20 [02:13<00:00,  6.67s/it]"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "download: s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00118039__2020-11-02T18_16_01-Measurement1/Images/r14c08f05p01-ch5sk1fk1fl1.tiff to figures/BRD4/U2OS/orf/PLK1/r14c08f05p01-ch5sk1fk1fl1.tiff\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "\n"
      ]
     }
    ],
@@ -379,7 +430,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|██████████| 18/18 [00:00<00:00, 70295.60it/s]\n"
+      "100%|██████████| 20/20 [00:42<00:00,  2.12s/it]\n"
      ]
     }
    ],
@@ -432,12 +483,12 @@
     "    \"A549\": {\n",
     "        \"compound\": [\"BI-2536\", \"PFI-1\", \"TG-101348\", \"DMSO\"],\n",
     "        \"crispr\": [\"BRD4\", \"PLK1\", \"crispr_control\"],\n",
-    "        \"orf\": [\"BRD4\", \"RB1\"],\n",
+    "        \"orf\": [\"BRD4\", \"PLK1\", \"RB1\"],\n",
     "    },\n",
     "    \"U2OS\": {\n",
     "        \"compound\": [\"BI-2536\", \"PFI-1\", \"TG-101348\", \"DMSO\"],\n",
     "        \"crispr\": [\"BRD4\", \"PLK1\", \"crispr_control\"],\n",
-    "        \"orf\": [\"BRD4\", \"RB1\"],\n",
+    "        \"orf\": [\"BRD4\", \"PLK1\", \"RB1\"],\n",
     "    },\n",
     "}\n",
     "\n",
@@ -456,7 +507,7 @@
     "\n",
     "        m = skimage.util.montage(\n",
     "            images,\n",
-    "            grid_shape=(3, 3),\n",
+    "            grid_shape=(4, 3),\n",
     "        )\n",
     "\n",
     "        skimage.io.imsave(f\"figures/BRD4/{cell_type}/{cell_type}_montage.png\", m)"