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‎demo-october-2022/ROIs_and_FeatureVis.ipynb‎

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{
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"cell_type": "code",
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"id": "fcf58b17-746c-4295-9fbe-f030567fb349",
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"id": "12dae7d5-0500-4442-a5f8-90dd20399b8a",
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{
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"cell_type": "code",
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"id": "9de6e678-889a-4a38-b748-6f70335d878a",
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"metadata": {},
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"id": "017efc23-ae9f-45cf-a713-1631bbccded7",
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"data": {
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" <thead>\n",
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" <tr style=\"text-align: right;\">\n",
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" <th></th>\n",
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" <th>x_micrometer</th>\n",
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" <th>y_micrometer</th>\n",
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" <th>z_micrometer</th>\n",
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" <th>len_x_micrometer</th>\n",
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" <th>len_y_micrometer</th>\n",
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" <th>len_z_micrometer</th>\n",
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" <th>x_micrometer_original</th>\n",
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" <th>y_micrometer_original</th>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>field_id</th>\n",
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" <th></th>\n",
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" </tr>\n",
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" </thead>\n",
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" <tbody>\n",
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" <tr>\n",
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" <th>FOV_1</th>\n",
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" <td>-1448.300049</td>\n",
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" <td>-1517.699951</td>\n",
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" <td>0.0</td>\n",
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" <th>FOV_2</th>\n",
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" <td>0.0</td>\n",
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" <td>-1517.699951</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>FOV_3</th>\n",
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" <td>-1448.300049</td>\n",
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" <td>-1166.699951</td>\n",
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" <td>0.0</td>\n",
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" <td>416.0</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>FOV_4</th>\n",
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],
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"text/plain": [
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" x_micrometer y_micrometer z_micrometer len_x_micrometer \\\n",
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"field_id \n",
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"FOV_1 -1448.300049 -1517.699951 0.0 416.0 \n",
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"FOV_2 -1032.300049 -1517.699951 0.0 416.0 \n",
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"FOV_3 -1448.300049 -1166.699951 0.0 416.0 \n",
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"FOV_4 -1032.300049 -1166.699951 0.0 416.0 \n",
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"\n",
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" len_y_micrometer len_z_micrometer x_micrometer_original \\\n",
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"field_id \n",
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"FOV_1 351.0 1.0 -1448.300049 \n",
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"FOV_2 351.0 1.0 -1032.300049 \n",
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"FOV_3 351.0 1.0 -1448.300049 \n",
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"FOV_4 351.0 1.0 -1032.300049 \n",
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"\n",
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" y_micrometer_original \n",
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"field_id \n",
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"FOV_1 -1517.699951 \n",
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"FOV_2 -1517.699951 \n",
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"FOV_3 -1166.699951 \n",
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"FOV_4 -1166.699951 "
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]
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},
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"execution_count": 4,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"# Look at the ROI table\n",
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"roi_an = ad.read_zarr(zarr_url / f'{well}/0/tables/{roi_table}')\n",
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"outputs": [
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{
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" <thead>\n",
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" <th></th>\n",
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" <th>area</th>\n",
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" <th>mean_intensity</th>\n",
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" <th>standard_deviation_intensity</th>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>label</th>\n",
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" </tr>\n",
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" <tbody>\n",
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" <th>1</th>\n",
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" <td>2128.0</td>\n",
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" <td>293.573792</td>\n",
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" <td>53.578331</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>2</th>\n",
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" <td>384.0</td>\n",
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" <td>311.109375</td>\n",
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" <td>106.931992</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>3</th>\n",
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" <td>1312.0</td>\n",
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" <td>231.229416</td>\n",
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" <td>47.511070</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>4</th>\n",
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" <td>2608.0</td>\n",
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" <td>264.913727</td>\n",
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" <td>57.151825</td>\n",
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" </tr>\n",
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" <th>5</th>\n",
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" <td>704.0</td>\n",
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" <td>387.032684</td>\n",
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" <td>176.512741</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>...</th>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" </tr>\n",
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" <th>2962</th>\n",
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" <td>1104.0</td>\n",
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" <td>75.626266</td>\n",
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" </tr>\n",
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" <td>296.225555</td>\n",
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" <td>73.479431</td>\n",
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" <td>736.0</td>\n",
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" <td>48.305725</td>\n",
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" </tr>\n",
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" <th>2965</th>\n",
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" <td>624.0</td>\n",
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" <td>204.426285</td>\n",
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" <td>44.935898</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>2966</th>\n",
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" <td>304.0</td>\n",
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" <td>247.736847</td>\n",
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" <td>56.399334</td>\n",
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" </tr>\n",
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" </tbody>\n",
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"</table>\n",
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"<p>2966 rows × 3 columns</p>\n",
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"</div>"
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],
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"text/plain": [
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" area mean_intensity standard_deviation_intensity\n",
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"label \n",
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"1 2128.0 293.573792 53.578331\n",
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"2 384.0 311.109375 106.931992\n",
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"3 1312.0 231.229416 47.511070\n",
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"4 2608.0 264.913727 57.151825\n",
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"5 704.0 387.032684 176.512741\n",
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"... ... ... ...\n",
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"2962 1104.0 311.662140 75.626266\n",
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"2963 1104.0 296.225555 73.479431\n",
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"2964 736.0 280.744568 48.305725\n",
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"2965 624.0 204.426285 44.935898\n",
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"2966 304.0 247.736847 56.399334\n",
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"\n",
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"[2966 rows x 3 columns]"
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]
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},
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"execution_count": 10,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"feature_df = nuclei_an.to_df()\n",
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"feature_df[['area', 'mean_intensity', 'standard_deviation_intensity']]"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 11,
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"id": "3d843d31-3f25-4553-b8b2-a447bc95e88e",
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"metadata": {},
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"outputs": [],

‎demo-october-2022/example_2x2_cardio_fmi/.fractal.env‎

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‎demo-october-2022/example_2x2_cardio_fmi/aux_extract_from_simple_json.py‎ renamed to ‎demo-october-2022/example_2x2_cardio_fmi/example_user/aux_extract_from_simple_json.py‎

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‎demo-october-2022/example_2x2_cardio_fmi/regionprops_from_existing_labels_feature.yaml‎ renamed to ‎demo-october-2022/example_2x2_cardio_fmi/example_user/regionprops_from_existing_labels_feature.yaml‎

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‎demo-october-2022/example_2x2_cardio_fmi/test_user/run_fractal_demo.sh‎ renamed to ‎demo-october-2022/example_2x2_cardio_fmi/example_user/run_fractal_demo.sh‎

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