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69 | 69 | },
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70 | 70 | {
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71 | 71 | "cell_type": "code",
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72 |
| - "execution_count": 1, |
| 72 | + "execution_count": null, |
73 | 73 | "metadata": {
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74 | 74 | "collapsed": true,
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75 | 75 | "id": "Y9weWEaezOmg"
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82 | 82 | },
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83 | 83 | {
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84 | 84 | "cell_type": "code",
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85 |
| - "execution_count": 2, |
| 85 | + "execution_count": null, |
86 | 86 | "metadata": {
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87 | 87 | "id": "YStGX-uGHUQa"
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88 | 88 | },
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107 | 107 | },
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108 | 108 | {
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109 | 109 | "cell_type": "code",
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110 |
| - "execution_count": 3, |
| 110 | + "execution_count": null, |
111 | 111 | "metadata": {
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112 | 112 | "colab": {
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113 | 113 | "base_uri": "https://localhost:8080/"
|
|
244 | 244 | "id": "8Ja50OuORgv9",
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245 | 245 | "outputId": "3778d0d9-da89-4760-db8a-ae9738f45591"
|
246 | 246 | },
|
247 |
| - "execution_count": 6, |
| 247 | + "execution_count": null, |
248 | 248 | "outputs": [
|
249 | 249 | {
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250 | 250 | "output_type": "display_data",
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563 | 563 | },
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564 | 564 | {
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565 | 565 | "cell_type": "code",
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566 |
| - "execution_count": 7, |
| 566 | + "execution_count": null, |
567 | 567 | "metadata": {
|
568 | 568 | "colab": {
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569 | 569 | "base_uri": "https://localhost:8080/",
|
|
895 | 895 | "id": "zYXInJorSTv9",
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896 | 896 | "outputId": "f4b4b58a-0aeb-4718-a784-57f606290d6e"
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897 | 897 | },
|
898 |
| - "execution_count": 8, |
| 898 | + "execution_count": null, |
899 | 899 | "outputs": [
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900 | 900 | {
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901 | 901 | "output_type": "stream",
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965 | 965 | "height": 313
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966 | 966 | }
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967 | 967 | },
|
968 |
| - "execution_count": 9, |
| 968 | + "execution_count": null, |
969 | 969 | "outputs": [
|
970 | 970 | {
|
971 | 971 | "output_type": "display_data",
|
|
1432 | 1432 | "base_uri": "https://localhost:8080/"
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1433 | 1433 | }
|
1434 | 1434 | },
|
1435 |
| - "execution_count": 10, |
| 1435 | + "execution_count": null, |
1436 | 1436 | "outputs": [
|
1437 | 1437 | {
|
1438 | 1438 | "output_type": "stream",
|
|
1466 | 1466 | "base_uri": "https://localhost:8080/"
|
1467 | 1467 | }
|
1468 | 1468 | },
|
1469 |
| - "execution_count": 11, |
| 1469 | + "execution_count": null, |
1470 | 1470 | "outputs": [
|
1471 | 1471 | {
|
1472 | 1472 | "output_type": "stream",
|
|
1490 | 1490 | },
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1491 | 1491 | {
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1492 | 1492 | "cell_type": "code",
|
1493 |
| - "execution_count": 12, |
| 1493 | + "execution_count": null, |
1494 | 1494 | "metadata": {
|
1495 | 1495 | "id": "z7U1q-EIL29P"
|
1496 | 1496 | },
|
|
1522 | 1522 | "id": "E_q86bgVLzO8"
|
1523 | 1523 | },
|
1524 | 1524 | "source": [
|
1525 |
| - "# Part 2: How to access and read whole-slide images from IDC" |
| 1525 | + "# Part 3: How to access and read whole-slide images from IDC" |
1526 | 1526 | ]
|
1527 | 1527 | },
|
1528 | 1528 | {
|
|
1536 | 1536 | },
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1537 | 1537 | {
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1538 | 1538 | "cell_type": "code",
|
1539 |
| - "execution_count": 13, |
| 1539 | + "execution_count": null, |
1540 | 1540 | "metadata": {
|
1541 | 1541 | "colab": {
|
1542 | 1542 | "base_uri": "https://localhost:8080/"
|
|
1572 | 1572 | },
|
1573 | 1573 | {
|
1574 | 1574 | "cell_type": "code",
|
1575 |
| - "execution_count": 14, |
| 1575 | + "execution_count": null, |
1576 | 1576 | "metadata": {
|
1577 | 1577 | "colab": {
|
1578 | 1578 | "base_uri": "https://localhost:8080/",
|
|
1961 | 1961 | },
|
1962 | 1962 | {
|
1963 | 1963 | "cell_type": "code",
|
1964 |
| - "execution_count": 15, |
| 1964 | + "execution_count": null, |
1965 | 1965 | "metadata": {
|
1966 | 1966 | "id": "E_eQc54DODUi",
|
1967 | 1967 | "colab": {
|
|
2092 | 2092 | "id": "0JT6sXgf7RFT"
|
2093 | 2093 | },
|
2094 | 2094 | "source": [
|
2095 |
| - "# Part 3: Application example -- Pre-trained model inference\n", |
| 2095 | + "# Part 4: Application example -- Pre-trained model inference\n", |
2096 | 2096 | "\n",
|
2097 | 2097 | "The TCGA-trained model that we use here was made available open source as part of the publication [The NCI Imaging Data Commons as a platform for reproducible research in computational pathology](https://doi.org/10.1016/j.cmpb.2023.107839). The specific model used here is a demo version, meaning that it was trained using slides at reduced magnification (pixel spacing of 0.002 mm/px instead of 0.001 mm/px) and will thus also be applied to slides at this resolution. The model is available as Github release asset and can be retrieved via curl."
|
2098 | 2098 | ]
|
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