diff --git a/examples/0.download_example_dataset.ipynb b/examples/0.download_example_dataset.ipynb
new file mode 100644
index 0000000..e213919
--- /dev/null
+++ b/examples/0.download_example_dataset.ipynb
@@ -0,0 +1,1705 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "b013fcef",
+   "metadata": {},
+   "source": [
+    "# Download JUMP pilot plate data from AWS S3 bucket for example training"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "6c8de60f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pathlib import Path\n",
+    "from urllib.parse import urlparse\n",
+    "\n",
+    "import pandas as pd\n",
+    "from sklearn.model_selection import train_test_split\n",
+    "\n",
+    "from virtual_stain_flow.datasets.example.cpjump1_manifest import get_manifest\n",
+    "from virtual_stain_flow.datasets.example.arrange_as_wide import arrange_manifest_channels"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c879dacc",
+   "metadata": {},
+   "source": [
+    "## Pathing"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d3baf91c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "DATA_DOWNLOAD_DIR = Path(\"/PATH/TO/WHERE/YOU/WANT/TO/DOWNLOAD/CPJUMP1\")\n",
+    "DATA_DOWNLOAD_DIR.mkdir(exist_ok=True, parents=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "63c8d005",
+   "metadata": {},
+   "source": [
+    "## S3 download helpers"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "6d789a28",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def _parse_s3_url(url):\n",
+    "    parsed = urlparse(url)\n",
+    "    if parsed.scheme != \"s3\":\n",
+    "        raise ValueError(f\"Expected s3:// URL, got: {url}\")\n",
+    "    return parsed.netloc, parsed.path.lstrip(\"/\")\n",
+    "\n",
+    "def download_wide_manifest_channels(\n",
+    "    wide_manifest,\n",
+    "    dest_dir,\n",
+    "    channel_columns=None,\n",
+    "    overwrite=False,\n",
+    "):\n",
+    "    \"\"\"\n",
+    "    Download S3 TIFFs for each channel and write a local file_index.csv with paths.\n",
+    "    \"\"\"\n",
+    "    if channel_columns is None:\n",
+    "        channel_columns = [\"LZ_BF\", \"BF\", \"HZ_BF\", \"DNA\", \"Mito\", \"AGP\", \"ER\", \"RNA\"]\n",
+    "    dest_dir = Path(dest_dir)\n",
+    "    dest_dir.mkdir(parents=True, exist_ok=True)\n",
+    "    try:\n",
+    "        import boto3\n",
+    "        from botocore import UNSIGNED\n",
+    "        from botocore.config import Config\n",
+    "    except ImportError as exc:\n",
+    "        raise ImportError(\n",
+    "            \"boto3 is required for S3 downloads. Install with: pip install boto3\"\n",
+    "        ) from exc\n",
+    "    s3 = boto3.client(\"s3\", config=Config(signature_version=UNSIGNED))\n",
+    "    local_rows = []\n",
+    "    for row_idx, row in wide_manifest.iterrows():\n",
+    "        prefix_parts = []\n",
+    "        for key in [\"Metadata_Plate\", \"Metadata_Well\", \"Metadata_Site\"]:\n",
+    "            if key in wide_manifest.columns:\n",
+    "                prefix_parts.append(str(row[key]))\n",
+    "        prefix = \"_\".join(prefix_parts) if prefix_parts else f\"row_{row_idx}\"\n",
+    "        local_row = {}\n",
+    "        for channel in channel_columns:\n",
+    "            url = row[channel] if channel in wide_manifest.columns else None\n",
+    "            if pd.isna(url):\n",
+    "                local_row[channel] = None\n",
+    "                continue\n",
+    "            bucket, key = _parse_s3_url(url)\n",
+    "            suffix = Path(key).suffix or \".tif\"\n",
+    "            local_path = dest_dir / f\"{prefix}_{channel}{suffix}\"\n",
+    "            if overwrite or not local_path.exists():\n",
+    "                s3.download_file(bucket, key, str(local_path))\n",
+    "            local_row[channel] = str(local_path)\n",
+    "        local_rows.append(local_row)\n",
+    "    file_index = pd.DataFrame(local_rows, columns=channel_columns)\n",
+    "    file_index.to_csv(dest_dir / \"file_index.csv\", index=False)\n",
+    "    return file_index\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8e5e7baf",
+   "metadata": {},
+   "source": [
+    "## Retrieve compound manifest"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "3452cbb4",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.microsoft.datawrangler.viewer.v0+json": {
+       "columns": [
+        {
+         "name": "index",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
+         "name": "Metadata_Well",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "broad_sample",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "solvent",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "InChIKey",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "pert_iname",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "pubchem_cid",
+         "rawType": "float64",
+         "type": "float"
+        },
+        {
+         "name": "target",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "target_list",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "pert_type",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "control_type",
+         "rawType": "object",
+         "type": "unknown"
+        },
+        {
+         "name": "smiles",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Batch",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Plate_Map_Name",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Metadata_Plate",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Perturbation",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Cell_type",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Time",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
+         "name": "Density",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
+         "name": "Antibiotics",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Cell_line",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Time_delay",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Times_imaged",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
+         "name": "Anomaly",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Number_of_images",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
+         "name": "Metadata_Site",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
+         "name": "Metadata_ChannelName",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Metadata_PlaneID",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
+         "name": "Metadata_PositionZ",
+         "rawType": "float64",
+         "type": "float"
+        },
+        {
+         "name": "Metadata_FileUrl",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Metadata_Filename",
+         "rawType": "object",
+         "type": "string"
+        }
+       ],
+       "ref": "6934d718-fb51-496b-99ce-57f0607bb381",
+       "rows": [
+        [
+         "0",
+         "A01",
+         "BRD-A86665761-001-01-1",
+         "DMSO",
+         "TZDUHAJSIBHXDL-UHFFFAOYSA-N",
+         "gabapentin-enacarbil",
+         "9883933.0",
+         "CACNB4",
+         "CACNA1A|CACNA1B|CACNA1C|CACNA1D|CACNA1E|CACNA1F|CACNA1G|CACNA1H|CACNA1I|CACNA1S|CACNA2D1|CACNA2D2|CACNA2D3|CACNA2D4|CACNB1|CACNB2|CACNB3|CACNB4|CACNG1|CACNG2|CACNG3|CACNG4|CACNG5|CACNG6|CACNG7|CACNG8",
+         "trt",
+         null,
+         "CC(C)C(=O)OC(C)OC(=O)NCC1(CC(O)=O)CCCCC1",
+         "2020_11_04_CPJUMP1",
+         "JUMP-Target-1_compound_platemap",
+         "BR00116991",
+         "compound",
+         "A549",
+         "24",
+         "100",
+         "absent",
+         "Parental",
+         "Day0",
+         "1",
+         "WGA",
+         "27648",
+         "1",
+         "DNA",
+         "1",
+         "-2e-06",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00116991__2020-11-05T19_51_35-Measurement1/Images/r01c01f01p01-ch5sk1fk1fl1.tiff",
+         "r01c01f01p01-ch5sk1fk1fl1.tiff"
+        ],
+        [
+         "1",
+         "A01",
+         "BRD-A86665761-001-01-1",
+         "DMSO",
+         "TZDUHAJSIBHXDL-UHFFFAOYSA-N",
+         "gabapentin-enacarbil",
+         "9883933.0",
+         "CACNB4",
+         "CACNA1A|CACNA1B|CACNA1C|CACNA1D|CACNA1E|CACNA1F|CACNA1G|CACNA1H|CACNA1I|CACNA1S|CACNA2D1|CACNA2D2|CACNA2D3|CACNA2D4|CACNB1|CACNB2|CACNB3|CACNB4|CACNG1|CACNG2|CACNG3|CACNG4|CACNG5|CACNG6|CACNG7|CACNG8",
+         "trt",
+         null,
+         "CC(C)C(=O)OC(C)OC(=O)NCC1(CC(O)=O)CCCCC1",
+         "2020_11_04_CPJUMP1",
+         "JUMP-Target-1_compound_platemap",
+         "BR00116991",
+         "compound",
+         "A549",
+         "24",
+         "100",
+         "absent",
+         "Parental",
+         "Day0",
+         "1",
+         "WGA",
+         "27648",
+         "2",
+         "DNA",
+         "1",
+         "-2e-06",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00116991__2020-11-05T19_51_35-Measurement1/Images/r01c01f02p01-ch5sk1fk1fl1.tiff",
+         "r01c01f02p01-ch5sk1fk1fl1.tiff"
+        ],
+        [
+         "2",
+         "A01",
+         "BRD-A86665761-001-01-1",
+         "DMSO",
+         "TZDUHAJSIBHXDL-UHFFFAOYSA-N",
+         "gabapentin-enacarbil",
+         "9883933.0",
+         "CACNB4",
+         "CACNA1A|CACNA1B|CACNA1C|CACNA1D|CACNA1E|CACNA1F|CACNA1G|CACNA1H|CACNA1I|CACNA1S|CACNA2D1|CACNA2D2|CACNA2D3|CACNA2D4|CACNB1|CACNB2|CACNB3|CACNB4|CACNG1|CACNG2|CACNG3|CACNG4|CACNG5|CACNG6|CACNG7|CACNG8",
+         "trt",
+         null,
+         "CC(C)C(=O)OC(C)OC(=O)NCC1(CC(O)=O)CCCCC1",
+         "2020_11_04_CPJUMP1",
+         "JUMP-Target-1_compound_platemap",
+         "BR00116991",
+         "compound",
+         "A549",
+         "24",
+         "100",
+         "absent",
+         "Parental",
+         "Day0",
+         "1",
+         "WGA",
+         "27648",
+         "3",
+         "DNA",
+         "1",
+         "-2e-06",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00116991__2020-11-05T19_51_35-Measurement1/Images/r01c01f03p01-ch5sk1fk1fl1.tiff",
+         "r01c01f03p01-ch5sk1fk1fl1.tiff"
+        ],
+        [
+         "3",
+         "A01",
+         "BRD-A86665761-001-01-1",
+         "DMSO",
+         "TZDUHAJSIBHXDL-UHFFFAOYSA-N",
+         "gabapentin-enacarbil",
+         "9883933.0",
+         "CACNB4",
+         "CACNA1A|CACNA1B|CACNA1C|CACNA1D|CACNA1E|CACNA1F|CACNA1G|CACNA1H|CACNA1I|CACNA1S|CACNA2D1|CACNA2D2|CACNA2D3|CACNA2D4|CACNB1|CACNB2|CACNB3|CACNB4|CACNG1|CACNG2|CACNG3|CACNG4|CACNG5|CACNG6|CACNG7|CACNG8",
+         "trt",
+         null,
+         "CC(C)C(=O)OC(C)OC(=O)NCC1(CC(O)=O)CCCCC1",
+         "2020_11_04_CPJUMP1",
+         "JUMP-Target-1_compound_platemap",
+         "BR00116991",
+         "compound",
+         "A549",
+         "24",
+         "100",
+         "absent",
+         "Parental",
+         "Day0",
+         "1",
+         "WGA",
+         "27648",
+         "4",
+         "DNA",
+         "1",
+         "-2e-06",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00116991__2020-11-05T19_51_35-Measurement1/Images/r01c01f04p01-ch5sk1fk1fl1.tiff",
+         "r01c01f04p01-ch5sk1fk1fl1.tiff"
+        ],
+        [
+         "4",
+         "A01",
+         "BRD-A86665761-001-01-1",
+         "DMSO",
+         "TZDUHAJSIBHXDL-UHFFFAOYSA-N",
+         "gabapentin-enacarbil",
+         "9883933.0",
+         "CACNB4",
+         "CACNA1A|CACNA1B|CACNA1C|CACNA1D|CACNA1E|CACNA1F|CACNA1G|CACNA1H|CACNA1I|CACNA1S|CACNA2D1|CACNA2D2|CACNA2D3|CACNA2D4|CACNB1|CACNB2|CACNB3|CACNB4|CACNG1|CACNG2|CACNG3|CACNG4|CACNG5|CACNG6|CACNG7|CACNG8",
+         "trt",
+         null,
+         "CC(C)C(=O)OC(C)OC(=O)NCC1(CC(O)=O)CCCCC1",
+         "2020_11_04_CPJUMP1",
+         "JUMP-Target-1_compound_platemap",
+         "BR00116991",
+         "compound",
+         "A549",
+         "24",
+         "100",
+         "absent",
+         "Parental",
+         "Day0",
+         "1",
+         "WGA",
+         "27648",
+         "5",
+         "DNA",
+         "1",
+         "-2e-06",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00116991__2020-11-05T19_51_35-Measurement1/Images/r01c01f05p01-ch5sk1fk1fl1.tiff",
+         "r01c01f05p01-ch5sk1fk1fl1.tiff"
+        ]
+       ],
+       "shape": {
+        "columns": 30,
+        "rows": 5
+       }
+      },
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>Metadata_Well</th>\n",
+       "      <th>broad_sample</th>\n",
+       "      <th>solvent</th>\n",
+       "      <th>InChIKey</th>\n",
+       "      <th>pert_iname</th>\n",
+       "      <th>pubchem_cid</th>\n",
+       "      <th>target</th>\n",
+       "      <th>target_list</th>\n",
+       "      <th>pert_type</th>\n",
+       "      <th>control_type</th>\n",
+       "      <th>...</th>\n",
+       "      <th>Time_delay</th>\n",
+       "      <th>Times_imaged</th>\n",
+       "      <th>Anomaly</th>\n",
+       "      <th>Number_of_images</th>\n",
+       "      <th>Metadata_Site</th>\n",
+       "      <th>Metadata_ChannelName</th>\n",
+       "      <th>Metadata_PlaneID</th>\n",
+       "      <th>Metadata_PositionZ</th>\n",
+       "      <th>Metadata_FileUrl</th>\n",
+       "      <th>Metadata_Filename</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>A01</td>\n",
+       "      <td>BRD-A86665761-001-01-1</td>\n",
+       "      <td>DMSO</td>\n",
+       "      <td>TZDUHAJSIBHXDL-UHFFFAOYSA-N</td>\n",
+       "      <td>gabapentin-enacarbil</td>\n",
+       "      <td>9883933.0</td>\n",
+       "      <td>CACNB4</td>\n",
+       "      <td>CACNA1A|CACNA1B|CACNA1C|CACNA1D|CACNA1E|CACNA1...</td>\n",
+       "      <td>trt</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>...</td>\n",
+       "      <td>Day0</td>\n",
+       "      <td>1</td>\n",
+       "      <td>WGA</td>\n",
+       "      <td>27648</td>\n",
+       "      <td>1</td>\n",
+       "      <td>DNA</td>\n",
+       "      <td>1</td>\n",
+       "      <td>-0.000002</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>r01c01f01p01-ch5sk1fk1fl1.tiff</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>A01</td>\n",
+       "      <td>BRD-A86665761-001-01-1</td>\n",
+       "      <td>DMSO</td>\n",
+       "      <td>TZDUHAJSIBHXDL-UHFFFAOYSA-N</td>\n",
+       "      <td>gabapentin-enacarbil</td>\n",
+       "      <td>9883933.0</td>\n",
+       "      <td>CACNB4</td>\n",
+       "      <td>CACNA1A|CACNA1B|CACNA1C|CACNA1D|CACNA1E|CACNA1...</td>\n",
+       "      <td>trt</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>...</td>\n",
+       "      <td>Day0</td>\n",
+       "      <td>1</td>\n",
+       "      <td>WGA</td>\n",
+       "      <td>27648</td>\n",
+       "      <td>2</td>\n",
+       "      <td>DNA</td>\n",
+       "      <td>1</td>\n",
+       "      <td>-0.000002</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>r01c01f02p01-ch5sk1fk1fl1.tiff</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>A01</td>\n",
+       "      <td>BRD-A86665761-001-01-1</td>\n",
+       "      <td>DMSO</td>\n",
+       "      <td>TZDUHAJSIBHXDL-UHFFFAOYSA-N</td>\n",
+       "      <td>gabapentin-enacarbil</td>\n",
+       "      <td>9883933.0</td>\n",
+       "      <td>CACNB4</td>\n",
+       "      <td>CACNA1A|CACNA1B|CACNA1C|CACNA1D|CACNA1E|CACNA1...</td>\n",
+       "      <td>trt</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>...</td>\n",
+       "      <td>Day0</td>\n",
+       "      <td>1</td>\n",
+       "      <td>WGA</td>\n",
+       "      <td>27648</td>\n",
+       "      <td>3</td>\n",
+       "      <td>DNA</td>\n",
+       "      <td>1</td>\n",
+       "      <td>-0.000002</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>r01c01f03p01-ch5sk1fk1fl1.tiff</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>A01</td>\n",
+       "      <td>BRD-A86665761-001-01-1</td>\n",
+       "      <td>DMSO</td>\n",
+       "      <td>TZDUHAJSIBHXDL-UHFFFAOYSA-N</td>\n",
+       "      <td>gabapentin-enacarbil</td>\n",
+       "      <td>9883933.0</td>\n",
+       "      <td>CACNB4</td>\n",
+       "      <td>CACNA1A|CACNA1B|CACNA1C|CACNA1D|CACNA1E|CACNA1...</td>\n",
+       "      <td>trt</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>...</td>\n",
+       "      <td>Day0</td>\n",
+       "      <td>1</td>\n",
+       "      <td>WGA</td>\n",
+       "      <td>27648</td>\n",
+       "      <td>4</td>\n",
+       "      <td>DNA</td>\n",
+       "      <td>1</td>\n",
+       "      <td>-0.000002</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>r01c01f04p01-ch5sk1fk1fl1.tiff</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>A01</td>\n",
+       "      <td>BRD-A86665761-001-01-1</td>\n",
+       "      <td>DMSO</td>\n",
+       "      <td>TZDUHAJSIBHXDL-UHFFFAOYSA-N</td>\n",
+       "      <td>gabapentin-enacarbil</td>\n",
+       "      <td>9883933.0</td>\n",
+       "      <td>CACNB4</td>\n",
+       "      <td>CACNA1A|CACNA1B|CACNA1C|CACNA1D|CACNA1E|CACNA1...</td>\n",
+       "      <td>trt</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>...</td>\n",
+       "      <td>Day0</td>\n",
+       "      <td>1</td>\n",
+       "      <td>WGA</td>\n",
+       "      <td>27648</td>\n",
+       "      <td>5</td>\n",
+       "      <td>DNA</td>\n",
+       "      <td>1</td>\n",
+       "      <td>-0.000002</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>r01c01f05p01-ch5sk1fk1fl1.tiff</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "<p>5 rows × 30 columns</p>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "  Metadata_Well            broad_sample solvent                     InChIKey  \\\n",
+       "0           A01  BRD-A86665761-001-01-1    DMSO  TZDUHAJSIBHXDL-UHFFFAOYSA-N   \n",
+       "1           A01  BRD-A86665761-001-01-1    DMSO  TZDUHAJSIBHXDL-UHFFFAOYSA-N   \n",
+       "2           A01  BRD-A86665761-001-01-1    DMSO  TZDUHAJSIBHXDL-UHFFFAOYSA-N   \n",
+       "3           A01  BRD-A86665761-001-01-1    DMSO  TZDUHAJSIBHXDL-UHFFFAOYSA-N   \n",
+       "4           A01  BRD-A86665761-001-01-1    DMSO  TZDUHAJSIBHXDL-UHFFFAOYSA-N   \n",
+       "\n",
+       "             pert_iname  pubchem_cid  target  \\\n",
+       "0  gabapentin-enacarbil    9883933.0  CACNB4   \n",
+       "1  gabapentin-enacarbil    9883933.0  CACNB4   \n",
+       "2  gabapentin-enacarbil    9883933.0  CACNB4   \n",
+       "3  gabapentin-enacarbil    9883933.0  CACNB4   \n",
+       "4  gabapentin-enacarbil    9883933.0  CACNB4   \n",
+       "\n",
+       "                                         target_list pert_type control_type  \\\n",
+       "0  CACNA1A|CACNA1B|CACNA1C|CACNA1D|CACNA1E|CACNA1...       trt          NaN   \n",
+       "1  CACNA1A|CACNA1B|CACNA1C|CACNA1D|CACNA1E|CACNA1...       trt          NaN   \n",
+       "2  CACNA1A|CACNA1B|CACNA1C|CACNA1D|CACNA1E|CACNA1...       trt          NaN   \n",
+       "3  CACNA1A|CACNA1B|CACNA1C|CACNA1D|CACNA1E|CACNA1...       trt          NaN   \n",
+       "4  CACNA1A|CACNA1B|CACNA1C|CACNA1D|CACNA1E|CACNA1...       trt          NaN   \n",
+       "\n",
+       "   ... Time_delay Times_imaged Anomaly Number_of_images Metadata_Site  \\\n",
+       "0  ...       Day0            1     WGA            27648             1   \n",
+       "1  ...       Day0            1     WGA            27648             2   \n",
+       "2  ...       Day0            1     WGA            27648             3   \n",
+       "3  ...       Day0            1     WGA            27648             4   \n",
+       "4  ...       Day0            1     WGA            27648             5   \n",
+       "\n",
+       "  Metadata_ChannelName  Metadata_PlaneID  Metadata_PositionZ  \\\n",
+       "0                  DNA                 1           -0.000002   \n",
+       "1                  DNA                 1           -0.000002   \n",
+       "2                  DNA                 1           -0.000002   \n",
+       "3                  DNA                 1           -0.000002   \n",
+       "4                  DNA                 1           -0.000002   \n",
+       "\n",
+       "                                    Metadata_FileUrl  \\\n",
+       "0  s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "1  s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "2  s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "3  s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "4  s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "\n",
+       "                Metadata_Filename  \n",
+       "0  r01c01f01p01-ch5sk1fk1fl1.tiff  \n",
+       "1  r01c01f02p01-ch5sk1fk1fl1.tiff  \n",
+       "2  r01c01f03p01-ch5sk1fk1fl1.tiff  \n",
+       "3  r01c01f04p01-ch5sk1fk1fl1.tiff  \n",
+       "4  r01c01f05p01-ch5sk1fk1fl1.tiff  \n",
+       "\n",
+       "[5 rows x 30 columns]"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "MANIFEST = get_manifest()\n",
+    "MANIFEST.head()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c62e8252",
+   "metadata": {},
+   "source": [
+    "## Filter manifest\n",
+    "For the sake of demoing training here we restricted timepoint to 24, and selected untreated U2-OS cells"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "82d77177",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.microsoft.datawrangler.viewer.v0+json": {
+       "columns": [
+        {
+         "name": "index",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
+         "name": "Metadata_Well",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "broad_sample",
+         "rawType": "object",
+         "type": "unknown"
+        },
+        {
+         "name": "solvent",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "InChIKey",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "pert_iname",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "pubchem_cid",
+         "rawType": "float64",
+         "type": "float"
+        },
+        {
+         "name": "target",
+         "rawType": "object",
+         "type": "unknown"
+        },
+        {
+         "name": "target_list",
+         "rawType": "object",
+         "type": "unknown"
+        },
+        {
+         "name": "pert_type",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "control_type",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "smiles",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Batch",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Plate_Map_Name",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Metadata_Plate",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Perturbation",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Cell_type",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Time",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
+         "name": "Density",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
+         "name": "Antibiotics",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Cell_line",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Time_delay",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Times_imaged",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
+         "name": "Anomaly",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Number_of_images",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
+         "name": "Metadata_Site",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
+         "name": "Metadata_ChannelName",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Metadata_PlaneID",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
+         "name": "Metadata_PositionZ",
+         "rawType": "float64",
+         "type": "float"
+        },
+        {
+         "name": "Metadata_FileUrl",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Metadata_Filename",
+         "rawType": "object",
+         "type": "string"
+        }
+       ],
+       "ref": "c4146cc9-71a6-40cc-ab80-c53a50b5f1e3",
+       "rows": [
+        [
+         "2312",
+         "A02",
+         null,
+         "DMSO",
+         "IAZDPXIOMUYVGZ-UHFFFAOYSA-N",
+         "DMSO",
+         "679.0",
+         null,
+         null,
+         "control",
+         "negcon",
+         "CS(=O)C",
+         "2020_11_04_CPJUMP1",
+         "JUMP-Target-1_compound_platemap",
+         "BR00117008",
+         "compound",
+         "A549",
+         "48",
+         "80",
+         "absent",
+         "Parental",
+         "Day0",
+         "1",
+         "none",
+         "27648",
+         "1",
+         "DNA",
+         "1",
+         "-2e-06",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f01p01-ch5sk1fk1fl1.tiff",
+         "r01c02f01p01-ch5sk1fk1fl1.tiff"
+        ],
+        [
+         "2313",
+         "A02",
+         null,
+         "DMSO",
+         "IAZDPXIOMUYVGZ-UHFFFAOYSA-N",
+         "DMSO",
+         "679.0",
+         null,
+         null,
+         "control",
+         "negcon",
+         "CS(=O)C",
+         "2020_11_04_CPJUMP1",
+         "JUMP-Target-1_compound_platemap",
+         "BR00117008",
+         "compound",
+         "A549",
+         "48",
+         "80",
+         "absent",
+         "Parental",
+         "Day0",
+         "1",
+         "none",
+         "27648",
+         "2",
+         "DNA",
+         "1",
+         "-2e-06",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f02p01-ch5sk1fk1fl1.tiff",
+         "r01c02f02p01-ch5sk1fk1fl1.tiff"
+        ],
+        [
+         "2314",
+         "A02",
+         null,
+         "DMSO",
+         "IAZDPXIOMUYVGZ-UHFFFAOYSA-N",
+         "DMSO",
+         "679.0",
+         null,
+         null,
+         "control",
+         "negcon",
+         "CS(=O)C",
+         "2020_11_04_CPJUMP1",
+         "JUMP-Target-1_compound_platemap",
+         "BR00117008",
+         "compound",
+         "A549",
+         "48",
+         "80",
+         "absent",
+         "Parental",
+         "Day0",
+         "1",
+         "none",
+         "27648",
+         "3",
+         "DNA",
+         "1",
+         "-2e-06",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f03p01-ch5sk1fk1fl1.tiff",
+         "r01c02f03p01-ch5sk1fk1fl1.tiff"
+        ],
+        [
+         "2315",
+         "A02",
+         null,
+         "DMSO",
+         "IAZDPXIOMUYVGZ-UHFFFAOYSA-N",
+         "DMSO",
+         "679.0",
+         null,
+         null,
+         "control",
+         "negcon",
+         "CS(=O)C",
+         "2020_11_04_CPJUMP1",
+         "JUMP-Target-1_compound_platemap",
+         "BR00117008",
+         "compound",
+         "A549",
+         "48",
+         "80",
+         "absent",
+         "Parental",
+         "Day0",
+         "1",
+         "none",
+         "27648",
+         "4",
+         "DNA",
+         "1",
+         "-2e-06",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f04p01-ch5sk1fk1fl1.tiff",
+         "r01c02f04p01-ch5sk1fk1fl1.tiff"
+        ],
+        [
+         "2316",
+         "A02",
+         null,
+         "DMSO",
+         "IAZDPXIOMUYVGZ-UHFFFAOYSA-N",
+         "DMSO",
+         "679.0",
+         null,
+         null,
+         "control",
+         "negcon",
+         "CS(=O)C",
+         "2020_11_04_CPJUMP1",
+         "JUMP-Target-1_compound_platemap",
+         "BR00117008",
+         "compound",
+         "A549",
+         "48",
+         "80",
+         "absent",
+         "Parental",
+         "Day0",
+         "1",
+         "none",
+         "27648",
+         "5",
+         "DNA",
+         "1",
+         "-2e-06",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f05p01-ch5sk1fk1fl1.tiff",
+         "r01c02f05p01-ch5sk1fk1fl1.tiff"
+        ]
+       ],
+       "shape": {
+        "columns": 30,
+        "rows": 5
+       }
+      },
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>Metadata_Well</th>\n",
+       "      <th>broad_sample</th>\n",
+       "      <th>solvent</th>\n",
+       "      <th>InChIKey</th>\n",
+       "      <th>pert_iname</th>\n",
+       "      <th>pubchem_cid</th>\n",
+       "      <th>target</th>\n",
+       "      <th>target_list</th>\n",
+       "      <th>pert_type</th>\n",
+       "      <th>control_type</th>\n",
+       "      <th>...</th>\n",
+       "      <th>Time_delay</th>\n",
+       "      <th>Times_imaged</th>\n",
+       "      <th>Anomaly</th>\n",
+       "      <th>Number_of_images</th>\n",
+       "      <th>Metadata_Site</th>\n",
+       "      <th>Metadata_ChannelName</th>\n",
+       "      <th>Metadata_PlaneID</th>\n",
+       "      <th>Metadata_PositionZ</th>\n",
+       "      <th>Metadata_FileUrl</th>\n",
+       "      <th>Metadata_Filename</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>2312</th>\n",
+       "      <td>A02</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>DMSO</td>\n",
+       "      <td>IAZDPXIOMUYVGZ-UHFFFAOYSA-N</td>\n",
+       "      <td>DMSO</td>\n",
+       "      <td>679.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>control</td>\n",
+       "      <td>negcon</td>\n",
+       "      <td>...</td>\n",
+       "      <td>Day0</td>\n",
+       "      <td>1</td>\n",
+       "      <td>none</td>\n",
+       "      <td>27648</td>\n",
+       "      <td>1</td>\n",
+       "      <td>DNA</td>\n",
+       "      <td>1</td>\n",
+       "      <td>-0.000002</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>r01c02f01p01-ch5sk1fk1fl1.tiff</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2313</th>\n",
+       "      <td>A02</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>DMSO</td>\n",
+       "      <td>IAZDPXIOMUYVGZ-UHFFFAOYSA-N</td>\n",
+       "      <td>DMSO</td>\n",
+       "      <td>679.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>control</td>\n",
+       "      <td>negcon</td>\n",
+       "      <td>...</td>\n",
+       "      <td>Day0</td>\n",
+       "      <td>1</td>\n",
+       "      <td>none</td>\n",
+       "      <td>27648</td>\n",
+       "      <td>2</td>\n",
+       "      <td>DNA</td>\n",
+       "      <td>1</td>\n",
+       "      <td>-0.000002</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>r01c02f02p01-ch5sk1fk1fl1.tiff</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2314</th>\n",
+       "      <td>A02</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>DMSO</td>\n",
+       "      <td>IAZDPXIOMUYVGZ-UHFFFAOYSA-N</td>\n",
+       "      <td>DMSO</td>\n",
+       "      <td>679.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>control</td>\n",
+       "      <td>negcon</td>\n",
+       "      <td>...</td>\n",
+       "      <td>Day0</td>\n",
+       "      <td>1</td>\n",
+       "      <td>none</td>\n",
+       "      <td>27648</td>\n",
+       "      <td>3</td>\n",
+       "      <td>DNA</td>\n",
+       "      <td>1</td>\n",
+       "      <td>-0.000002</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>r01c02f03p01-ch5sk1fk1fl1.tiff</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2315</th>\n",
+       "      <td>A02</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>DMSO</td>\n",
+       "      <td>IAZDPXIOMUYVGZ-UHFFFAOYSA-N</td>\n",
+       "      <td>DMSO</td>\n",
+       "      <td>679.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>control</td>\n",
+       "      <td>negcon</td>\n",
+       "      <td>...</td>\n",
+       "      <td>Day0</td>\n",
+       "      <td>1</td>\n",
+       "      <td>none</td>\n",
+       "      <td>27648</td>\n",
+       "      <td>4</td>\n",
+       "      <td>DNA</td>\n",
+       "      <td>1</td>\n",
+       "      <td>-0.000002</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>r01c02f04p01-ch5sk1fk1fl1.tiff</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2316</th>\n",
+       "      <td>A02</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>DMSO</td>\n",
+       "      <td>IAZDPXIOMUYVGZ-UHFFFAOYSA-N</td>\n",
+       "      <td>DMSO</td>\n",
+       "      <td>679.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>control</td>\n",
+       "      <td>negcon</td>\n",
+       "      <td>...</td>\n",
+       "      <td>Day0</td>\n",
+       "      <td>1</td>\n",
+       "      <td>none</td>\n",
+       "      <td>27648</td>\n",
+       "      <td>5</td>\n",
+       "      <td>DNA</td>\n",
+       "      <td>1</td>\n",
+       "      <td>-0.000002</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>r01c02f05p01-ch5sk1fk1fl1.tiff</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "<p>5 rows × 30 columns</p>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "     Metadata_Well broad_sample solvent                     InChIKey  \\\n",
+       "2312           A02          NaN    DMSO  IAZDPXIOMUYVGZ-UHFFFAOYSA-N   \n",
+       "2313           A02          NaN    DMSO  IAZDPXIOMUYVGZ-UHFFFAOYSA-N   \n",
+       "2314           A02          NaN    DMSO  IAZDPXIOMUYVGZ-UHFFFAOYSA-N   \n",
+       "2315           A02          NaN    DMSO  IAZDPXIOMUYVGZ-UHFFFAOYSA-N   \n",
+       "2316           A02          NaN    DMSO  IAZDPXIOMUYVGZ-UHFFFAOYSA-N   \n",
+       "\n",
+       "     pert_iname  pubchem_cid target target_list pert_type control_type  ...  \\\n",
+       "2312       DMSO        679.0    NaN         NaN   control       negcon  ...   \n",
+       "2313       DMSO        679.0    NaN         NaN   control       negcon  ...   \n",
+       "2314       DMSO        679.0    NaN         NaN   control       negcon  ...   \n",
+       "2315       DMSO        679.0    NaN         NaN   control       negcon  ...   \n",
+       "2316       DMSO        679.0    NaN         NaN   control       negcon  ...   \n",
+       "\n",
+       "     Time_delay Times_imaged Anomaly Number_of_images Metadata_Site  \\\n",
+       "2312       Day0            1    none            27648             1   \n",
+       "2313       Day0            1    none            27648             2   \n",
+       "2314       Day0            1    none            27648             3   \n",
+       "2315       Day0            1    none            27648             4   \n",
+       "2316       Day0            1    none            27648             5   \n",
+       "\n",
+       "     Metadata_ChannelName  Metadata_PlaneID  Metadata_PositionZ  \\\n",
+       "2312                  DNA                 1           -0.000002   \n",
+       "2313                  DNA                 1           -0.000002   \n",
+       "2314                  DNA                 1           -0.000002   \n",
+       "2315                  DNA                 1           -0.000002   \n",
+       "2316                  DNA                 1           -0.000002   \n",
+       "\n",
+       "                                       Metadata_FileUrl  \\\n",
+       "2312  s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "2313  s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "2314  s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "2315  s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "2316  s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "\n",
+       "                   Metadata_Filename  \n",
+       "2312  r01c02f01p01-ch5sk1fk1fl1.tiff  \n",
+       "2313  r01c02f02p01-ch5sk1fk1fl1.tiff  \n",
+       "2314  r01c02f03p01-ch5sk1fk1fl1.tiff  \n",
+       "2315  r01c02f04p01-ch5sk1fk1fl1.tiff  \n",
+       "2316  r01c02f05p01-ch5sk1fk1fl1.tiff  \n",
+       "\n",
+       "[5 rows x 30 columns]"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "negcon_a549_48_manifest = MANIFEST[\n",
+    "    (MANIFEST[\"Cell_type\"] == \"A549\") &\n",
+    "    (MANIFEST[\"Anomaly\"] == \"none\") &\n",
+    "    (MANIFEST[\"control_type\"] == 'negcon') &\n",
+    "    (MANIFEST[\"Time\"] == 48)\n",
+    "]\n",
+    "negcon_a549_48_manifest.head()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6b4431f0",
+   "metadata": {},
+   "source": [
+    "## Arrange as wide is the anticipated format in virtual stain flow datasets and also the format the download helper expects this format"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "952e2717",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.microsoft.datawrangler.viewer.v0+json": {
+       "columns": [
+        {
+         "name": "index",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
+         "name": "Metadata_Plate",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Metadata_Well",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Metadata_Site",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
+         "name": "LZ_BF",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "BF",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "HZ_BF",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "DNA",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "Mito",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "AGP",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "ER",
+         "rawType": "object",
+         "type": "string"
+        },
+        {
+         "name": "RNA",
+         "rawType": "object",
+         "type": "string"
+        }
+       ],
+       "ref": "a6710032-e5c6-41b0-a361-af52c8cb0633",
+       "rows": [
+        [
+         "0",
+         "BR00117008",
+         "A02",
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+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f01p01-ch8sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f01p01-ch6sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f01p01-ch5sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f01p01-ch1sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f01p01-ch2sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f01p01-ch4sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f01p01-ch3sk1fk1fl1.tiff"
+        ],
+        [
+         "1",
+         "BR00117008",
+         "A02",
+         "2",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f02p01-ch7sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f02p01-ch8sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f02p01-ch6sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f02p01-ch5sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f02p01-ch1sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f02p01-ch2sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f02p01-ch4sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f02p01-ch3sk1fk1fl1.tiff"
+        ],
+        [
+         "2",
+         "BR00117008",
+         "A02",
+         "3",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f03p01-ch7sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f03p01-ch8sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f03p01-ch6sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f03p01-ch5sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f03p01-ch1sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f03p01-ch2sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f03p01-ch4sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f03p01-ch3sk1fk1fl1.tiff"
+        ],
+        [
+         "3",
+         "BR00117008",
+         "A02",
+         "4",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f04p01-ch7sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f04p01-ch8sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f04p01-ch6sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f04p01-ch5sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f04p01-ch1sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f04p01-ch2sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f04p01-ch4sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f04p01-ch3sk1fk1fl1.tiff"
+        ],
+        [
+         "4",
+         "BR00117008",
+         "A02",
+         "5",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f05p01-ch7sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f05p01-ch8sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f05p01-ch6sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f05p01-ch5sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f05p01-ch1sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f05p01-ch2sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f05p01-ch4sk1fk1fl1.tiff",
+         "s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/BR00117008__2020-11-09T00_55_40-Measurement1/Images/r01c02f05p01-ch3sk1fk1fl1.tiff"
+        ]
+       ],
+       "shape": {
+        "columns": 11,
+        "rows": 5
+       }
+      },
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th>Metadata_ChannelName</th>\n",
+       "      <th>Metadata_Plate</th>\n",
+       "      <th>Metadata_Well</th>\n",
+       "      <th>Metadata_Site</th>\n",
+       "      <th>LZ_BF</th>\n",
+       "      <th>BF</th>\n",
+       "      <th>HZ_BF</th>\n",
+       "      <th>DNA</th>\n",
+       "      <th>Mito</th>\n",
+       "      <th>AGP</th>\n",
+       "      <th>ER</th>\n",
+       "      <th>RNA</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>BR00117008</td>\n",
+       "      <td>A02</td>\n",
+       "      <td>1</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>BR00117008</td>\n",
+       "      <td>A02</td>\n",
+       "      <td>2</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>BR00117008</td>\n",
+       "      <td>A02</td>\n",
+       "      <td>3</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>BR00117008</td>\n",
+       "      <td>A02</td>\n",
+       "      <td>4</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>BR00117008</td>\n",
+       "      <td>A02</td>\n",
+       "      <td>5</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "      <td>s3://cellpainting-gallery/cpg0000-jump-pilot/s...</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "Metadata_ChannelName Metadata_Plate Metadata_Well  Metadata_Site  \\\n",
+       "0                        BR00117008           A02              1   \n",
+       "1                        BR00117008           A02              2   \n",
+       "2                        BR00117008           A02              3   \n",
+       "3                        BR00117008           A02              4   \n",
+       "4                        BR00117008           A02              5   \n",
+       "\n",
+       "Metadata_ChannelName                                              LZ_BF  \\\n",
+       "0                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "1                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "2                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "3                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "4                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "\n",
+       "Metadata_ChannelName                                                 BF  \\\n",
+       "0                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "1                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "2                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "3                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "4                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "\n",
+       "Metadata_ChannelName                                              HZ_BF  \\\n",
+       "0                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "1                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "2                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "3                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "4                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "\n",
+       "Metadata_ChannelName                                                DNA  \\\n",
+       "0                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "1                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "2                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "3                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "4                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "\n",
+       "Metadata_ChannelName                                               Mito  \\\n",
+       "0                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "1                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "2                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "3                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "4                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "\n",
+       "Metadata_ChannelName                                                AGP  \\\n",
+       "0                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "1                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "2                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "3                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "4                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "\n",
+       "Metadata_ChannelName                                                 ER  \\\n",
+       "0                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "1                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "2                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "3                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "4                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...   \n",
+       "\n",
+       "Metadata_ChannelName                                                RNA  \n",
+       "0                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...  \n",
+       "1                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...  \n",
+       "2                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...  \n",
+       "3                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...  \n",
+       "4                     s3://cellpainting-gallery/cpg0000-jump-pilot/s...  "
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "wide_manifest = arrange_manifest_channels(negcon_a549_48_manifest)\n",
+    "wide_manifest.head()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d62c00e5",
+   "metadata": {},
+   "source": [
+    "## Data split"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "848fd839",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Train plates: 9, Test plates: 3\n",
+      "Train samples: 6974, Test samples: 1728\n"
+     ]
+    }
+   ],
+   "source": [
+    "a549_data_dir = DATA_DOWNLOAD_DIR / \"cpjump1_a549_48h\"\n",
+    "a549_data_dir.mkdir(exist_ok=True, parents=True)\n",
+    "\n",
+    "# Get unique plates\n",
+    "unique_plates = wide_manifest['Metadata_Plate'].unique()\n",
+    "\n",
+    "# Split plates into train (75%) and test (25%) with seed\n",
+    "train_plates, test_plates = train_test_split(\n",
+    "    unique_plates, \n",
+    "    test_size=0.25, \n",
+    "    random_state=42\n",
+    ")\n",
+    "\n",
+    "# Create train and test manifests based on plate split\n",
+    "train_manifest_wide = wide_manifest[wide_manifest['Metadata_Plate'].isin(train_plates)]\n",
+    "test_manifest_wide = wide_manifest[wide_manifest['Metadata_Plate'].isin(test_plates)]\n",
+    "\n",
+    "print(f\"Train plates: {len(train_plates)}, Test plates: {len(test_plates)}\")\n",
+    "print(f\"Train samples: {len(train_manifest_wide)}, Test samples: {len(test_manifest_wide)}\")\n",
+    "\n",
+    "negcon_a549_48_manifest.to_csv(a549_data_dir / \"raw_manifest.csv\", index=False)\n",
+    "train_manifest_wide.to_csv(a549_data_dir/ \"train_manifest.csv\", index=False)\n",
+    "test_manifest_wide.to_csv(a549_data_dir / \"test_manifest.csv\", index=False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "70d2ff65",
+   "metadata": {},
+   "source": [
+    "## Download all data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "010575e5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "_ = download_wide_manifest_channels(\n",
+    "    train_manifest_wide,\n",
+    "    dest_dir = a549_data_dir / \"train\"    \n",
+    ")\n",
+    "_ = download_wide_manifest_channels(\n",
+    "    test_manifest_wide,\n",
+    "    dest_dir = a549_data_dir / \"test\"    \n",
+    ")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "virtual_stain_flow",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/examples/nbconverted/0.download_example_dataset.py b/examples/nbconverted/0.download_example_dataset.py
new file mode 100644
index 0000000..3fc359c
--- /dev/null
+++ b/examples/nbconverted/0.download_example_dataset.py
@@ -0,0 +1,162 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+# # Download JUMP pilot plate data from AWS S3 bucket for example training
+
+# In[1]:
+
+
+from pathlib import Path
+from urllib.parse import urlparse
+
+import pandas as pd
+from sklearn.model_selection import train_test_split
+
+from virtual_stain_flow.datasets.example.cpjump1_manifest import get_manifest
+from virtual_stain_flow.datasets.example.arrange_as_wide import arrange_manifest_channels
+
+
+# ## Pathing
+
+# In[ ]:
+
+
+DATA_DOWNLOAD_DIR = Path("/PATH/TO/WHERE/YOU/WANT/TO/DOWNLOAD/CPJUMP1")
+DATA_DOWNLOAD_DIR.mkdir(exist_ok=True, parents=True)
+
+
+# ## S3 download helpers
+
+# In[3]:
+
+
+def _parse_s3_url(url):
+    parsed = urlparse(url)
+    if parsed.scheme != "s3":
+        raise ValueError(f"Expected s3:// URL, got: {url}")
+    return parsed.netloc, parsed.path.lstrip("/")
+
+def download_wide_manifest_channels(
+    wide_manifest,
+    dest_dir,
+    channel_columns=None,
+    overwrite=False,
+):
+    """
+    Download S3 TIFFs for each channel and write a local file_index.csv with paths.
+    """
+    if channel_columns is None:
+        channel_columns = ["LZ_BF", "BF", "HZ_BF", "DNA", "Mito", "AGP", "ER", "RNA"]
+    dest_dir = Path(dest_dir)
+    dest_dir.mkdir(parents=True, exist_ok=True)
+    try:
+        import boto3
+        from botocore import UNSIGNED
+        from botocore.config import Config
+    except ImportError as exc:
+        raise ImportError(
+            "boto3 is required for S3 downloads. Install with: pip install boto3"
+        ) from exc
+    s3 = boto3.client("s3", config=Config(signature_version=UNSIGNED))
+    local_rows = []
+    for row_idx, row in wide_manifest.iterrows():
+        prefix_parts = []
+        for key in ["Metadata_Plate", "Metadata_Well", "Metadata_Site"]:
+            if key in wide_manifest.columns:
+                prefix_parts.append(str(row[key]))
+        prefix = "_".join(prefix_parts) if prefix_parts else f"row_{row_idx}"
+        local_row = {}
+        for channel in channel_columns:
+            url = row[channel] if channel in wide_manifest.columns else None
+            if pd.isna(url):
+                local_row[channel] = None
+                continue
+            bucket, key = _parse_s3_url(url)
+            suffix = Path(key).suffix or ".tif"
+            local_path = dest_dir / f"{prefix}_{channel}{suffix}"
+            if overwrite or not local_path.exists():
+                s3.download_file(bucket, key, str(local_path))
+            local_row[channel] = str(local_path)
+        local_rows.append(local_row)
+    file_index = pd.DataFrame(local_rows, columns=channel_columns)
+    file_index.to_csv(dest_dir / "file_index.csv", index=False)
+    return file_index
+
+
+# ## Retrieve compound manifest
+
+# In[4]:
+
+
+MANIFEST = get_manifest()
+MANIFEST.head()
+
+
+# ## Filter manifest
+# For the sake of demoing training here we restricted timepoint to 24, and selected untreated U2-OS cells
+
+# In[5]:
+
+
+negcon_a549_48_manifest = MANIFEST[
+    (MANIFEST["Cell_type"] == "A549") &
+    (MANIFEST["Anomaly"] == "none") &
+    (MANIFEST["control_type"] == 'negcon') &
+    (MANIFEST["Time"] == 48)
+]
+negcon_a549_48_manifest.head()
+
+
+# ## Arrange as wide is the anticipated format in virtual stain flow datasets and also the format the download helper expects this format
+
+# In[6]:
+
+
+wide_manifest = arrange_manifest_channels(negcon_a549_48_manifest)
+wide_manifest.head()
+
+
+# ## Data split
+
+# In[7]:
+
+
+a549_data_dir = DATA_DOWNLOAD_DIR / "cpjump1_a549_48h"
+a549_data_dir.mkdir(exist_ok=True, parents=True)
+
+# Get unique plates
+unique_plates = wide_manifest['Metadata_Plate'].unique()
+
+# Split plates into train (75%) and test (25%) with seed
+train_plates, test_plates = train_test_split(
+    unique_plates, 
+    test_size=0.25, 
+    random_state=42
+)
+
+# Create train and test manifests based on plate split
+train_manifest_wide = wide_manifest[wide_manifest['Metadata_Plate'].isin(train_plates)]
+test_manifest_wide = wide_manifest[wide_manifest['Metadata_Plate'].isin(test_plates)]
+
+print(f"Train plates: {len(train_plates)}, Test plates: {len(test_plates)}")
+print(f"Train samples: {len(train_manifest_wide)}, Test samples: {len(test_manifest_wide)}")
+
+negcon_a549_48_manifest.to_csv(a549_data_dir / "raw_manifest.csv", index=False)
+train_manifest_wide.to_csv(a549_data_dir/ "train_manifest.csv", index=False)
+test_manifest_wide.to_csv(a549_data_dir / "test_manifest.csv", index=False)
+
+
+# ## Download all data
+
+# In[ ]:
+
+
+_ = download_wide_manifest_channels(
+    train_manifest_wide,
+    dest_dir = a549_data_dir / "train"    
+)
+_ = download_wide_manifest_channels(
+    test_manifest_wide,
+    dest_dir = a549_data_dir / "test"    
+)
+
diff --git a/pyproject.toml b/pyproject.toml
index 1dfdd8a..2f7b3dd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -30,6 +30,7 @@ dependencies = [
   "notebook",
   "tifffile",
   "pandera[pandas]",
+  "boto3"
 ]
 
 [project.optional-dependencies]
diff --git a/src/virtual_stain_flow/datasets/example/arrange_as_wide.py b/src/virtual_stain_flow/datasets/example/arrange_as_wide.py
new file mode 100644
index 0000000..f150bf3
--- /dev/null
+++ b/src/virtual_stain_flow/datasets/example/arrange_as_wide.py
@@ -0,0 +1,32 @@
+"""
+Helper utility specifically to support the example CPJUMP1 dataset 
+    pivoting and arranging as file index.
+"""
+
+import pandas as pd
+
+
+def arrange_manifest_channels(manifest):
+    """
+    Return a wide dataframe with one row per plate/well/site and URL columns per channel.
+    """
+    required_channels = ["LZ_BF", "BF", "HZ_BF", "DNA", "Mito", "AGP", "ER", "RNA"]
+    keys = ["Metadata_Plate", "Metadata_Well", "Metadata_Site"]
+    filtered = manifest[manifest["Metadata_ChannelName"].isin(required_channels)].copy()
+    filtered["Metadata_ChannelName"] = filtered["Metadata_ChannelName"].astype(
+        pd.CategoricalDtype(categories=required_channels, ordered=True)
+    )
+    filtered = filtered.sort_values(keys + ["Metadata_ChannelName"])
+    wide = (
+        filtered.pivot_table(
+            index=keys,
+            columns="Metadata_ChannelName",
+            values="Metadata_FileUrl",
+            aggfunc="first",
+            observed=False,
+        )
+        .reindex(columns=required_channels)
+        .reset_index()
+    )
+    
+    return wide
diff --git a/src/virtual_stain_flow/datasets/example/cpjump1_manifest.py b/src/virtual_stain_flow/datasets/example/cpjump1_manifest.py
new file mode 100644
index 0000000..cd45a8b
--- /dev/null
+++ b/src/virtual_stain_flow/datasets/example/cpjump1_manifest.py
@@ -0,0 +1,144 @@
+"""Build an enriched image manifest for CPJUMP1 dataset access.
+
+Only compound perturbations (no CRISPR or ORF) are included, which is
+appropriate for virtual staining experiments.
+"""
+
+from __future__ import annotations
+
+import argparse
+import sys
+from typing import Optional
+
+import pandas as pd
+
+# Most recent commit ref as of Mar 25 2026.
+REPO_REF = "6ea3958c3809cd04ac95b63138937dd64a7c4c12"
+REPO_BASE = f"https://github.com/WayScience/JUMP-single-cell/raw/{REPO_REF}/"
+
+IMAGE_MANIFEST_URL = f"{REPO_BASE}0.download_data/data/2020_11_04_CPJUMP1_all_plates.parquet"
+IMAGE_MANIFEST_COLUMNS = [
+    "Metadata_Plate",
+    "Metadata_Well",
+    "Metadata_Site",
+    "Metadata_ChannelName",
+    "Metadata_PlaneID",
+    "Metadata_PositionZ",
+    "Metadata_FileUrl",
+    "Metadata_Filename",
+]
+
+EXPERIMENT_METADATA_URL = f"{REPO_BASE}reference_plate_data/experiment-metadata.tsv"
+COMPOUND_PLATEMAP_URL = f"{REPO_BASE}reference_plate_data/JUMP-Target-1_compound_platemap.txt"
+COMPOUND_METADATA_URL = f"{REPO_BASE}reference_plate_data/JUMP-Target-1_compound_metadata_targets.tsv"
+
+__all__ = ["build_manifest", "get_manifest", "main"]
+
+_MANIFEST_CACHE: Optional[pd.DataFrame] = None
+
+
+def build_manifest() -> pd.DataFrame:
+    """
+    Main utility function that handles all the wrangling. 
+    Return an enriched CPJUMP1 manifest as a pandas DataFrame.
+    """
+    image_manifest = pd.read_parquet(IMAGE_MANIFEST_URL, columns=IMAGE_MANIFEST_COLUMNS)
+
+    experiment_meta = pd.read_csv(EXPERIMENT_METADATA_URL, delimiter="\t")
+    experiment_meta.rename(columns={"Assay_Plate_Barcode": "Metadata_Plate"}, inplace=True)
+    experiment_meta = experiment_meta[experiment_meta["Perturbation"] == "compound"]
+    # exclude dl batch which is essentially duplicate in context for image data access
+    experiment_meta = experiment_meta[~experiment_meta["Batch"].str.endswith("_DL")]
+
+    compound_platemap = pd.merge(
+        pd.read_csv(COMPOUND_PLATEMAP_URL, delimiter="\t"),
+        pd.read_csv(COMPOUND_METADATA_URL, delimiter="\t"),
+        on="broad_sample",
+        how="left",
+        validate="many_to_one"    
+    ).rename(columns={"well_position": "Metadata_Well"}, inplace=False)
+
+    image_manifest_compound = pd.merge(
+        experiment_meta,
+        image_manifest,
+        on="Metadata_Plate",
+        how="inner",
+        validate="one_to_many" # one plate id should map to many image rows
+    )
+
+    return pd.merge(
+        compound_platemap,
+        image_manifest_compound,
+        on="Metadata_Well",
+        how="inner",
+        # all the plates share the same well map so one well should map to many image rows
+        validate="one_to_many" 
+    )
+
+
+def get_manifest() -> pd.DataFrame:
+    """
+    Return a cached manifest to avoid repeated network reads.
+    """
+    global _MANIFEST_CACHE
+    if _MANIFEST_CACHE is None:
+        _MANIFEST_CACHE = build_manifest()
+    return _MANIFEST_CACHE
+
+
+def _write_manifest(df: pd.DataFrame, output: str, fmt: str) -> None:
+    if fmt == "csv":
+        df.to_csv(output, index=False)
+    elif fmt == "parquet":
+        df.to_parquet(output, index=False)
+    else:
+        raise ValueError(f"Unsupported format: {fmt}")
+
+
+def main(argv: Optional[list[str]] = None) -> int:
+    """
+    Command-line interface to building and outputting the CPJUMP1 manifest.
+    By default, it prints a summary and preview of the manifest. 
+    Use --output or --stdout to write the full manifest to a file or stdout.
+    """
+    parser = argparse.ArgumentParser(description="Build CPJUMP1 enriched manifest.")
+    parser.add_argument(
+        "--output",
+        help="Write manifest to a file (CSV or Parquet).",
+    )
+    parser.add_argument(
+        "--format",
+        choices=["csv", "parquet"],
+        default="csv",
+        help="Output file format when using --output (default: csv).",
+    )
+    parser.add_argument(
+        "--stdout",
+        action="store_true",
+        help="Write manifest to stdout as CSV.",
+    )
+    parser.add_argument(
+        "--head",
+        type=int,
+        default=5,
+        help="Rows to display when no output is specified (default: 5).",
+    )
+    args = parser.parse_args(argv)
+
+    manifest = get_manifest()
+
+    if args.stdout:
+        manifest.to_csv(sys.stdout, index=False)
+        return 0
+
+    if args.output:
+        _write_manifest(manifest, args.output, args.format)
+        return 0
+
+    print(f"Rows: {len(manifest):,} | Columns: {len(manifest.columns)}")
+    print(manifest.head(args.head).to_string(index=False))
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())