|
69 | 69 | }, |
70 | 70 | { |
71 | 71 | "cell_type": "code", |
72 | | - "execution_count": 1, |
| 72 | + "execution_count": null, |
73 | 73 | "metadata": { |
74 | 74 | "collapsed": true, |
75 | 75 | "id": "Y9weWEaezOmg" |
|
82 | 82 | }, |
83 | 83 | { |
84 | 84 | "cell_type": "code", |
85 | | - "execution_count": 2, |
| 85 | + "execution_count": null, |
86 | 86 | "metadata": { |
87 | 87 | "id": "YStGX-uGHUQa" |
88 | 88 | }, |
|
107 | 107 | }, |
108 | 108 | { |
109 | 109 | "cell_type": "code", |
110 | | - "execution_count": 3, |
| 110 | + "execution_count": null, |
111 | 111 | "metadata": { |
112 | 112 | "colab": { |
113 | 113 | "base_uri": "https://localhost:8080/" |
|
244 | 244 | "id": "8Ja50OuORgv9", |
245 | 245 | "outputId": "3778d0d9-da89-4760-db8a-ae9738f45591" |
246 | 246 | }, |
247 | | - "execution_count": 6, |
| 247 | + "execution_count": null, |
248 | 248 | "outputs": [ |
249 | 249 | { |
250 | 250 | "output_type": "display_data", |
|
563 | 563 | }, |
564 | 564 | { |
565 | 565 | "cell_type": "code", |
566 | | - "execution_count": 7, |
| 566 | + "execution_count": null, |
567 | 567 | "metadata": { |
568 | 568 | "colab": { |
569 | 569 | "base_uri": "https://localhost:8080/", |
|
895 | 895 | "id": "zYXInJorSTv9", |
896 | 896 | "outputId": "f4b4b58a-0aeb-4718-a784-57f606290d6e" |
897 | 897 | }, |
898 | | - "execution_count": 8, |
| 898 | + "execution_count": null, |
899 | 899 | "outputs": [ |
900 | 900 | { |
901 | 901 | "output_type": "stream", |
|
965 | 965 | "height": 313 |
966 | 966 | } |
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/" |
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 | }, |
1491 | 1491 | { |
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 | }, |
1537 | 1537 | { |
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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