From 2332287cc6fa63ae6fd0a1c199e4bfc5b47c5a0e Mon Sep 17 00:00:00 2001 From: erindiel Date: Tue, 22 Oct 2024 14:17:31 -0400 Subject: [PATCH 1/3] use idc-index and smaller files for conversion examples --- .../IDC_Recipes_Conversion.ipynb | 1754 +---------------- 1 file changed, 43 insertions(+), 1711 deletions(-) diff --git a/notebooks/advanced_topics/IDC_Recipes_Conversion.ipynb b/notebooks/advanced_topics/IDC_Recipes_Conversion.ipynb index 616fc6d..272804b 100644 --- a/notebooks/advanced_topics/IDC_Recipes_Conversion.ipynb +++ b/notebooks/advanced_topics/IDC_Recipes_Conversion.ipynb @@ -33,7 +33,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": { "colab": { "base_uri": "https://localhost:8080/" @@ -41,64 +41,13 @@ "id": "X0zL0c6qAzVO", "outputId": "0b56702c-43ee-4cc2-b2ec-639b8ee88bae" }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Collecting s5cmd\n", - " Using cached s5cmd-0.2.0-py3-none-macosx_11_0_arm64.whl.metadata (5.7 kB)\n", - "Using cached s5cmd-0.2.0-py3-none-macosx_11_0_arm64.whl (4.7 MB)\n", - "Installing collected packages: s5cmd\n", - "Successfully installed s5cmd-0.2.0\n", - "--2024-06-06 16:05:48-- https://downloads.openmicroscopy.org/bio-formats/7.3.0/artifacts/bftools.zip\n", - "Resolving downloads.openmicroscopy.org (downloads.openmicroscopy.org)... 134.36.65.239\n", - "Connecting to downloads.openmicroscopy.org (downloads.openmicroscopy.org)|134.36.65.239|:443... connected.\n", - "HTTP request sent, awaiting response... 200 OK\n", - "Length: 42518871 (41M) [application/zip]\n", - "Saving to: ‘bftools.zip’\n", - "\n", - "bftools.zip 100%[===================>] 40.55M 2.42MB/s in 21s \n", - "\n", - "2024-06-06 16:06:10 (1.93 MB/s) - ‘bftools.zip’ saved [42518871/42518871]\n", - "\n", - "Archive: bftools.zip\n", - " creating: bftools/\n", - " inflating: bftools/bf-unconfigured.bat \n", - " inflating: bftools/bf.bat \n", - " inflating: bftools/bfconvert.bat \n", - " inflating: bftools/config.bat \n", - " inflating: bftools/config.sh \n", - " inflating: bftools/domainlist.bat \n", - " inflating: bftools/formatlist.bat \n", - " inflating: bftools/ijview.bat \n", - " inflating: bftools/logback.xml \n", - " inflating: bftools/mkfake.bat \n", - " inflating: bftools/showinf.bat \n", - " inflating: bftools/tiffcomment.bat \n", - " inflating: bftools/xmlindent.bat \n", - " inflating: bftools/xmlvalid.bat \n", - " inflating: bftools/bf-unconfigured \n", - " inflating: bftools/bf.sh \n", - " inflating: bftools/bfconvert \n", - " inflating: bftools/domainlist \n", - " inflating: bftools/formatlist \n", - " inflating: bftools/ijview \n", - " inflating: bftools/mkfake \n", - " inflating: bftools/showinf \n", - " inflating: bftools/tiffcomment \n", - " inflating: bftools/xmlindent \n", - " inflating: bftools/xmlvalid \n", - " inflating: bftools/bioformats_package.jar \n" - ] - } - ], + "outputs": [], "source": [ "# IDC supports image download via s5cmd\n", - "!pip install s5cmd\n", + "!pip install idc-index\n", "\n", "# Install bfconvert via bftools\n", - "!wget https://downloads.openmicroscopy.org/bio-formats/7.3.0/artifacts/bftools.zip\n", + "!wget https://downloads.openmicroscopy.org/bio-formats/latest/artifacts/bftools.zip\n", "!unzip bftools.zip\n" ] }, @@ -112,14 +61,12 @@ "\n", "Explore and download IDC data here: https://portal.imaging.datacommons.cancer.gov/explore/\n", "\n", - "Examples below used [TCGA-ACC](https://portal.imaging.datacommons.cancer.gov/explore/filters/?Modality_op=OR&Modality=SM&collection_id=tcga_acc)\n", - "\n", "OpenSlide also provides sample data in various whole slide image formats, including [SVS](https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/) for the examples below." ] }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": { "colab": { "base_uri": "https://localhost:8080/" @@ -127,53 +74,13 @@ "id": "ghc9vCGFHwCo", "outputId": "5c645fc7-9753-4dfc-d178-cfbfde90d57e" }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "cp s3://idc-open-data/6d7f4ec7-2c84-4a46-86ac-acde279195bb/49cbd3fa-638d-4da2-9432-54d71fcf7dd0.dcm rgb-dicom/49cbd3fa-638d-4da2-9432-54d71fcf7dd0.dcm\n", - "cp s3://idc-open-data/6d7f4ec7-2c84-4a46-86ac-acde279195bb/d2031780-db50-49bc-b2b0-186213fedb34.dcm rgb-dicom/d2031780-db50-49bc-b2b0-186213fedb34.dcm\n", - "cp s3://idc-open-data/6d7f4ec7-2c84-4a46-86ac-acde279195bb/74527996-46d8-4f42-af90-4b87c41a66f1.dcm rgb-dicom/74527996-46d8-4f42-af90-4b87c41a66f1.dcm\n", - "cp s3://idc-open-data/6d7f4ec7-2c84-4a46-86ac-acde279195bb/e0076901-151f-43dd-8f56-9e2adec521da.dcm rgb-dicom/e0076901-151f-43dd-8f56-9e2adec521da.dcm\n", - "cp s3://idc-open-data/6d7f4ec7-2c84-4a46-86ac-acde279195bb/5ee2770f-b222-4565-a3bd-46ba294ca222.dcm rgb-dicom/5ee2770f-b222-4565-a3bd-46ba294ca222.dcm\n", - "--2024-06-06 16:09:37-- https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1-Small-Region.svs\n", - "Resolving openslide.cs.cmu.edu (openslide.cs.cmu.edu)... 128.2.209.93\n", - "Connecting to openslide.cs.cmu.edu (openslide.cs.cmu.edu)|128.2.209.93|:443... connected.\n", - "HTTP request sent, awaiting response... 200 OK\n", - "Length: 1938955 (1.8M) [image/tiff]\n", - "Saving to: ‘rgb-svs/CMU-1-Small-Region.svs’\n", - "\n", - "CMU-1-Small-Region. 100%[===================>] 1.85M 1.51MB/s in 1.2s \n", - "\n", - "2024-06-06 16:09:38 (1.51 MB/s) - ‘rgb-svs/CMU-1-Small-Region.svs’ saved [1938955/1938955]\n", - "\n", - "rgb-dicom/:\n", - "total 2781536\n", - "drwxr-xr-x@ 7 erindiel staff 224B Jun 6 16:09 \u001b[34m.\u001b[m\u001b[m\n", - "drwxr-xr-x 10 erindiel staff 320B Jun 6 16:09 \u001b[34m..\u001b[m\u001b[m\n", - "-rw-r--r--@ 1 erindiel staff 6.3M Jun 6 16:09 49cbd3fa-638d-4da2-9432-54d71fcf7dd0.dcm\n", - "-rw-r--r--@ 1 erindiel staff 1.1G Jun 6 16:09 5ee2770f-b222-4565-a3bd-46ba294ca222.dcm\n", - "-rw-r--r--@ 1 erindiel staff 1.6M Jun 6 16:09 74527996-46d8-4f42-af90-4b87c41a66f1.dcm\n", - "-rw-r--r--@ 1 erindiel staff 19M Jun 6 16:09 d2031780-db50-49bc-b2b0-186213fedb34.dcm\n", - "-rw-r--r--@ 1 erindiel staff 177M Jun 6 16:09 e0076901-151f-43dd-8f56-9e2adec521da.dcm\n", - "\n", - "rgb-svs/:\n", - "total 4648\n", - "drwxr-xr-x@ 3 erindiel staff 96B Jun 6 16:09 \u001b[34m.\u001b[m\u001b[m\n", - "drwxr-xr-x 10 erindiel staff 320B Jun 6 16:09 \u001b[34m..\u001b[m\u001b[m\n", - "-rw-r--r--@ 1 erindiel staff 1.8M Dec 6 2013 CMU-1-Small-Region.svs\n" - ] - } - ], + "outputs": [], "source": [ "# Download sample data from IDC\n", - "!s5cmd --no-sign-request --endpoint-url https://s3.amazonaws.com cp \"s3://idc-open-data/6d7f4ec7-2c84-4a46-86ac-acde279195bb/*\" rgb-dicom\n", + "!idc download 1.3.6.1.4.1.5962.99.1.1999040126.632533787.1655561481854.4.0\n", "\n", "# Download sample data from OpenSlide\n", - "!wget https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1-Small-Region.svs --directory-prefix rgb-svs\n", - "\n", - "!ls -lah rgb*/\n" + "!wget https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1-Small-Region.svs --directory-prefix rgb-svs\n" ] }, { @@ -187,7 +94,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": { "colab": { "base_uri": "https://localhost:8080/" @@ -195,27 +102,7 @@ "id": "NJLk8Jfg9RwG", "outputId": "83785187-5a7b-41de-bb64-baeea4ac2918" }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "rgb-svs/CMU-1-Small-Region.svs\n", - "SVSReader initializing rgb-svs/CMU-1-Small-Region.svs\n", - "Reading IFDs\n", - "Populating metadata\n", - "Populating OME metadata\n", - "[Aperio SVS] -> rgb-svs/CMU-1-Small-Region.dcm [DICOM]\n", - "\tSeries 0: converted 1/1 planes (100%)\n", - "Decompressed tile: series=1, resolution=0, x=0, y=0\n", - "\tSeries 1: converted 1/1 planes (100%)\n", - "Decompressed tile: series=2, resolution=0, x=0, y=0\n", - "\tSeries 2: converted 1/1 planes (100%)\n", - "[done]\n", - "0.606s elapsed (30.333334+38.666668ms per plane, 286ms overhead)\n" - ] - } - ], + "outputs": [], "source": [ "# Convert SVS to DICOM with precompressed tiles\n", "# This will copy tiles from the original SVS, so tile sizes do not need to be specified\n", @@ -229,7 +116,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": { "colab": { "base_uri": "https://localhost:8080/" @@ -237,61 +124,17 @@ "id": "FSforIqg-hOb", "outputId": "8fae398e-91c6-4756-9da7-876ebc6a2d71" }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "rgb-dicom/5ee2770f-b222-4565-a3bd-46ba294ca222.dcm\n", - "DicomReader initializing rgb-dicom/5ee2770f-b222-4565-a3bd-46ba294ca222.dcm\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "[DICOM] -> rgb-dicom/output.ome.tiff [OME-TIFF]\n", - "Tile size = 512 x 512\n", - "\tConverted 1/1 planes (100%)\n", - "[done]\n", - "3.466s elapsed (66.0+321.0ms per plane, 2888ms overhead)\n" - ] - } - ], + "outputs": [], "source": [ "# Convert DICOM to OME-TIFF without precompressed tiles\n", "\n", "# Convert using bfconvert with non-default options:\n", - "# Crop the full resolution image and drop the resolution pyramid because the output image is small\n", - "# A 1000x1000 region of the full resolution image starting at (5000,5000) will be converted.\n", - "\n", "# Tile sizes do not need to be specified if the tile dimensions in the original DICOM should be preserved,\n", "# but here tiles are explicitly set to 512x512 to demonstrate the '-tilex' and '-tiley' options.\n", "\n", - "# If converting the entire input dataset instead:\n", - "# - omit the '-crop 5000,5000,1000,1000' option\n", - "# - replace the '-series 0' option with '-noflat'\n", + "# Choose a single .dcm file as the input\n", "\n", - "!./bftools/bfconvert -series 0 -compression JPEG-2000 -crop 5000,5000,1000,1000 -overwrite -tilex 512 -tiley 512 rgb-dicom/5ee2770f-b222-4565-a3bd-46ba294ca222.dcm rgb-dicom/output.ome.tiff\n" + "!./bftools/bfconvert -compression JPEG-2000 -overwrite -tilex 512 -tiley 512 htan_wustl/HTA12_11/2.25.66963730400918147916879305140687405342/SM_1.3.6.1.4.1.5962.99.1.1999040126.632533787.1655561481854.4.0/8def879c-e010-4abf-b0d7-82893142232f.dcm htan_wustl/output.ome.tiff\n" ] }, { @@ -302,7 +145,9 @@ "source": [ "## Conversion using bioformats2raw, raw2ometiff and NGFF-Converter\n", "\n", - "There are also several tools which make use of Bio-Formats, and can be used to convert to either [OME-NGFF/OME-Zarr](https://ngff.openmicroscopy.org/latest/index.html) or OME-TIFF. These include the [bioformats2raw](https://github.com/glencoesoftware/bioformats2raw) command line tool, which converts any input format supported by Bio-Formats to OME-NGFF/OME-Zarr, and [raw2ometiff](https://github.com/glencoesoftware/raw2ometiff), which converts OME-NGFF/OME-Zarr to OME-TIFF." + "There are also several tools which make use of Bio-Formats, and can be used to convert to either [OME-NGFF/OME-Zarr](https://ngff.openmicroscopy.org/latest/index.html) or OME-TIFF. These include the [bioformats2raw](https://github.com/glencoesoftware/bioformats2raw) command line tool, which converts any input format supported by Bio-Formats to OME-NGFF/OME-Zarr, and [raw2ometiff](https://github.com/glencoesoftware/raw2ometiff), which converts OME-NGFF/OME-Zarr to OME-TIFF.\n", + "\n", + "Note that this notebook should be run locally for optimal performance, rather than using Google Colab. See [here](https://github.com/glencoesoftware/bioformats2raw/issues?tab=readme-ov-file#performance) for more information on conversion performance." ] }, { @@ -316,7 +161,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": { "colab": { "base_uri": "https://localhost:8080/" @@ -324,250 +169,12 @@ "id": "DD5QpTworu3M", "outputId": "0da37e4e-93f0-490e-97df-d77d98506437" }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "--2024-06-06 16:10:44-- https://github.com/glencoesoftware/bioformats2raw/releases/download/v0.9.3/bioformats2raw-0.9.3.zip\n", - "Resolving github.com (github.com)... 140.82.112.3\n", - "Connecting to github.com (github.com)|140.82.112.3|:443... connected.\n", - "HTTP request sent, awaiting response... 302 Found\n", - "Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/213945032/e986a6d1-978c-4b53-9c8a-d87522e18292?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=releaseassetproduction%2F20240606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20240606T201044Z&X-Amz-Expires=300&X-Amz-Signature=46f0910d4cd0c89689dabeddbeb464b9c6206d5324d8d62d3f23fb9d56a1640f&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=213945032&response-content-disposition=attachment%3B%20filename%3Dbioformats2raw-0.9.3.zip&response-content-type=application%2Foctet-stream [following]\n", - "--2024-06-06 16:10:44-- https://objects.githubusercontent.com/github-production-release-asset-2e65be/213945032/e986a6d1-978c-4b53-9c8a-d87522e18292?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=releaseassetproduction%2F20240606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20240606T201044Z&X-Amz-Expires=300&X-Amz-Signature=46f0910d4cd0c89689dabeddbeb464b9c6206d5324d8d62d3f23fb9d56a1640f&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=213945032&response-content-disposition=attachment%3B%20filename%3Dbioformats2raw-0.9.3.zip&response-content-type=application%2Foctet-stream\n", - "Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.109.133, 185.199.111.133, 185.199.108.133, ...\n", - "Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.109.133|:443... connected.\n", - "HTTP request sent, awaiting response... 200 OK\n", - "Length: 171375305 (163M) [application/octet-stream]\n", - "Saving to: ‘bioformats2raw-0.9.3.zip’\n", - 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" inflating: bioformats2raw-0.9.3/lib/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar \n", - " inflating: bioformats2raw-0.9.3/lib/checker-qual-3.33.0.jar \n", - " inflating: bioformats2raw-0.9.3/lib/error_prone_annotations-2.18.0.jar \n", - " inflating: bioformats2raw-0.9.3/lib/j2objc-annotations-2.8.jar \n", - " inflating: bioformats2raw-0.9.3/lib/okhttp-3.7.0.jar \n", - " inflating: bioformats2raw-0.9.3/lib/okio-1.12.0.jar \n", - " inflating: bioformats2raw-0.9.3/lib/ome-jai-0.1.4.jar \n", - " inflating: bioformats2raw-0.9.3/lib/aircompressor-0.21.jar \n", - " inflating: bioformats2raw-0.9.3/lib/jgoodies-common-1.7.0.jar \n", - " inflating: bioformats2raw-0.9.3/lib/base-18.09.0.jar \n", - " inflating: bioformats2raw-0.9.3/lib/commons-io-2.7.jar \n", - " inflating: bioformats2raw-0.9.3/lib/commons-lang3-3.10.jar \n", - " inflating: bioformats2raw-0.9.3/lib/xmpcore-6.1.11.jar \n", - " inflating: bioformats2raw-0.9.3/lib/hamcrest-core-1.3.jar \n", - " inflating: bioformats2raw-0.9.3/lib/ion-java-1.0.2.jar \n", - " inflating: bioformats2raw-0.9.3/lib/xpp3-1.1.4c.jar \n", - " inflating: bioformats2raw-0.9.3/lib/commons-codec-1.11.jar \n", - " creating: bioformats2raw-0.9.3/bin/\n", - " inflating: bioformats2raw-0.9.3/bin/bioformats2raw \n", - " inflating: bioformats2raw-0.9.3/bin/bioformats2raw.bat \n", - " inflating: bioformats2raw-0.9.3/README.md \n", - " inflating: bioformats2raw-0.9.3/LICENSE.txt \n", - "--2024-06-06 16:10:48-- https://github.com/glencoesoftware/raw2ometiff/releases/download/v0.7.1/raw2ometiff-0.7.1.zip\n", - "Resolving github.com (github.com)... 140.82.112.3\n", - "Connecting to github.com (github.com)|140.82.112.3|:443... connected.\n", - "HTTP request sent, awaiting response... 302 Found\n", - "Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/213945909/e761e8d9-46c8-4b11-b34e-c72bd8238793?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=releaseassetproduction%2F20240606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20240606T201048Z&X-Amz-Expires=300&X-Amz-Signature=08ee8aa42bcc4ba392ec7ccc92c54f3d9446bfebef9504678817165847271fc8&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=213945909&response-content-disposition=attachment%3B%20filename%3Draw2ometiff-0.7.1.zip&response-content-type=application%2Foctet-stream [following]\n", - "--2024-06-06 16:10:48-- https://objects.githubusercontent.com/github-production-release-asset-2e65be/213945909/e761e8d9-46c8-4b11-b34e-c72bd8238793?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=releaseassetproduction%2F20240606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20240606T201048Z&X-Amz-Expires=300&X-Amz-Signature=08ee8aa42bcc4ba392ec7ccc92c54f3d9446bfebef9504678817165847271fc8&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=213945909&response-content-disposition=attachment%3B%20filename%3Draw2ometiff-0.7.1.zip&response-content-type=application%2Foctet-stream\n", - "Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.109.133, 185.199.111.133, 185.199.108.133, ...\n", - "Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.109.133|:443... connected.\n", - "HTTP request sent, awaiting response... 200 OK\n", - "Length: 171399194 (163M) [application/octet-stream]\n", - "Saving to: ‘raw2ometiff-0.7.1.zip’\n", - "\n", - "raw2ometiff-0.7.1.z 100%[===================>] 163.46M 70.4MB/s in 2.3s \n", - "\n", - "2024-06-06 16:10:51 (70.4 MB/s) - ‘raw2ometiff-0.7.1.zip’ saved [171399194/171399194]\n", - "\n", - "Archive: raw2ometiff-0.7.1.zip\n", - " creating: raw2ometiff-0.7.1/\n", - " creating: raw2ometiff-0.7.1/lib/\n", - " creating: raw2ometiff-0.7.1/lib/config/\n", - " inflating: raw2ometiff-0.7.1/lib/config/logback.xml \n", - " inflating: raw2ometiff-0.7.1/lib/raw2ometiff-0.7.1.jar \n", - " inflating: raw2ometiff-0.7.1/lib/bioformats2raw-0.9.2.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jzarr-0.4.2.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jblosc-1.0.1.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jna-5.10.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/picocli-4.7.5.jar \n", - " inflating: raw2ometiff-0.7.1/lib/progressbar-0.9.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/formats-gpl-7.2.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/formats-bsd-7.3.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/logback-classic-1.3.14.jar \n", - " inflating: raw2ometiff-0.7.1/lib/logback-core-1.3.14.jar \n", - " inflating: raw2ometiff-0.7.1/lib/cdm-core-5.3.3.jar \n", - " inflating: raw2ometiff-0.7.1/lib/formats-api-7.3.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/ome-xml-6.3.6.jar \n", - " inflating: raw2ometiff-0.7.1/lib/ome-codecs-1.0.3.jar \n", - " inflating: raw2ometiff-0.7.1/lib/metakit-5.3.5.jar \n", - " inflating: raw2ometiff-0.7.1/lib/ome-poi-5.3.7.jar \n", - " inflating: raw2ometiff-0.7.1/lib/ome-common-6.0.22.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jackson-annotations-2.14.2.jar \n", - " inflating: raw2ometiff-0.7.1/lib/s3fs-2.2.3.jar \n", - " inflating: raw2ometiff-0.7.1/lib/aws-java-sdk-s3-1.11.232.jar \n", - " inflating: raw2ometiff-0.7.1/lib/aws-java-sdk-kms-1.11.232.jar \n", - " inflating: raw2ometiff-0.7.1/lib/aws-java-sdk-core-1.11.232.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jackson-dataformat-cbor-2.14.2.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jackson-core-2.14.2.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jmespath-java-1.11.232.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jackson-databind-2.14.2.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jline-3.16.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/specification-6.3.6.jar \n", - " inflating: raw2ometiff-0.7.1/lib/turbojpeg-7.3.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jxrlib-all-0.2.4.jar \n", - " inflating: raw2ometiff-0.7.1/lib/native-lib-loader-2.4.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jgoodies-forms-1.7.2.jar \n", - " inflating: raw2ometiff-0.7.1/lib/kryo-5.4.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/commons-lang-2.6.jar \n", - " inflating: raw2ometiff-0.7.1/lib/perf4j-0.9.16.jar \n", - " inflating: raw2ometiff-0.7.1/lib/udunits-5.3.3.jar \n", - " inflating: raw2ometiff-0.7.1/lib/httpservices-5.3.3.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jcl-over-slf4j-1.7.5.jar \n", - " inflating: raw2ometiff-0.7.1/lib/slf4j-api-2.0.9.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jhdf5-19.04.1.jar \n", - " inflating: raw2ometiff-0.7.1/lib/metadata-extractor-2.18.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/json-20231013.jar \n", - " inflating: raw2ometiff-0.7.1/lib/xercesImpl-2.12.2.jar \n", - " inflating: raw2ometiff-0.7.1/lib/xml-apis-1.4.01.jar \n", - " inflating: raw2ometiff-0.7.1/lib/serializer-2.7.3.jar \n", - " inflating: raw2ometiff-0.7.1/lib/xalan-2.7.3.jar \n", - " inflating: raw2ometiff-0.7.1/lib/snakeyaml-2.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/univocity-parsers-2.8.4.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jaxb-api-2.3.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/opencv-4.7.0-0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/minio-5.0.2.jar \n", - " inflating: raw2ometiff-0.7.1/lib/joda-time-2.12.2.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jdom2-2.0.6.jar \n", - " inflating: raw2ometiff-0.7.1/lib/guava-32.0.0-jre.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jsr305-3.0.2.jar \n", - " inflating: raw2ometiff-0.7.1/lib/protobuf-java-3.9.1.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jcommander-1.78.jar \n", - " inflating: raw2ometiff-0.7.1/lib/httpmime-4.5.9.jar \n", - " inflating: raw2ometiff-0.7.1/lib/google-http-client-xml-1.20.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/google-http-client-1.20.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/httpclient-4.5.9.jar \n", - " inflating: raw2ometiff-0.7.1/lib/httpcore-4.4.11.jar \n", - " inflating: raw2ometiff-0.7.1/lib/re2j-1.3.jar \n", - " inflating: raw2ometiff-0.7.1/lib/junit-4.12.jar \n", - " inflating: raw2ometiff-0.7.1/lib/ome-jai-0.1.4.jar \n", - " inflating: raw2ometiff-0.7.1/lib/aircompressor-0.21.jar \n", - " inflating: raw2ometiff-0.7.1/lib/jgoodies-common-1.7.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/reflectasm-1.11.9.jar \n", - " inflating: raw2ometiff-0.7.1/lib/objenesis-3.3.jar \n", - " inflating: raw2ometiff-0.7.1/lib/minlog-1.3.1.jar \n", - " inflating: raw2ometiff-0.7.1/lib/base-18.09.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/commons-io-2.7.jar \n", - " inflating: raw2ometiff-0.7.1/lib/commons-lang3-3.10.jar \n", - " inflating: raw2ometiff-0.7.1/lib/xmpcore-6.1.11.jar \n", - " inflating: raw2ometiff-0.7.1/lib/ome-mdbtools-5.3.2.jar \n", - " inflating: raw2ometiff-0.7.1/lib/sqlite-jdbc-3.28.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/tika-core-1.5.jar \n", - " inflating: raw2ometiff-0.7.1/lib/hamcrest-core-1.3.jar \n", - " inflating: raw2ometiff-0.7.1/lib/failureaccess-1.0.1.jar \n", - " inflating: raw2ometiff-0.7.1/lib/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar \n", - " inflating: raw2ometiff-0.7.1/lib/checker-qual-3.33.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/error_prone_annotations-2.18.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/j2objc-annotations-2.8.jar \n", - " inflating: raw2ometiff-0.7.1/lib/okhttp-3.7.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/okio-1.12.0.jar \n", - " inflating: raw2ometiff-0.7.1/lib/commons-logging-1.2.jar \n", - " inflating: raw2ometiff-0.7.1/lib/commons-codec-1.11.jar \n", - " inflating: raw2ometiff-0.7.1/lib/xpp3-1.1.4c.jar \n", - " inflating: raw2ometiff-0.7.1/lib/ion-java-1.0.2.jar \n", - " creating: raw2ometiff-0.7.1/bin/\n", - " inflating: raw2ometiff-0.7.1/bin/raw2ometiff.bat \n", - " inflating: raw2ometiff-0.7.1/bin/raw2ometiff \n", - " inflating: raw2ometiff-0.7.1/README.md \n", - " inflating: raw2ometiff-0.7.1/LICENSE.txt \n" - ] - } - ], + "outputs": [], "source": [ "# Download and unzip bioformats2raw and raw2ometiff\n", "\n", - "!wget https://github.com/glencoesoftware/bioformats2raw/releases/download/v0.9.3/bioformats2raw-0.9.3.zip\n", - "!unzip bioformats2raw-0.9.3.zip\n", + "!wget https://github.com/glencoesoftware/bioformats2raw/releases/download/v0.9.4/bioformats2raw-0.9.4.zip\n", + "!unzip bioformats2raw-0.9.4.zip\n", "\n", "!wget https://github.com/glencoesoftware/raw2ometiff/releases/download/v0.7.1/raw2ometiff-0.7.1.zip\n", "!unzip raw2ometiff-0.7.1.zip\n" @@ -584,24 +191,11 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": { "id": "kyrI4551Eqq2" }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "2024-06-06 16:27:47,539 [main] WARN c.g.bioformats2raw.Converter - Overwriting output path rgb-dicom/output.zarr\n", - "WARNING: An illegal reflective access operation has occurred\n", - "WARNING: Illegal reflective access by com.esotericsoftware.reflectasm.AccessClassLoader (file:/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/bioformats2raw-0.9.3/lib/reflectasm-1.11.9.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)\n", - "WARNING: Please consider reporting this to the maintainers of com.esotericsoftware.reflectasm.AccessClassLoader\n", - "WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations\n", - "WARNING: All illegal access operations will be denied in a future release\n" - ] - } - ], + "outputs": [], "source": [ "# Convert DICOM to OME-TIFF with bioformats2raw/raw2ometiff default options\n", "# The resulting OME-TIFF will use LZW compression, so is likely to be much larger than the input data.\n", @@ -610,40 +204,28 @@ "# Follow instructions here for Blosc installation: https://github.com/glencoesoftware/bioformats2raw/?tab=readme-ov-file#requirements\n", "# OR add \"--compression zlib\" to the \"bioformats2raw\" command below\n", "\n", - "!./bioformats2raw-0.9.3/bin/bioformats2raw rgb-dicom/5ee2770f-b222-4565-a3bd-46ba294ca222.dcm rgb-dicom/output.zarr --overwrite\n", - "#!./bioformats2raw-0.9.3/bin/bioformats2raw rgb-dicom/5ee2770f-b222-4565-a3bd-46ba294ca222.dcm rgb-dicom/output.zarr --overwrite --compression zlib\n", - "!./raw2ometiff-0.7.1/bin/raw2ometiff rgb-dicom/output.zarr rgb-dicom/output-default.ome.tiff\n" + "# Use a single .dcm file as input\n", + "\n", + "!./bioformats2raw-0.9.4/bin/bioformats2raw htan_wustl/HTA12_11/2.25.66963730400918147916879305140687405342/SM_1.3.6.1.4.1.5962.99.1.1999040126.632533787.1655561481854.4.0/8def879c-e010-4abf-b0d7-82893142232f.dcm htan_wustl/output.zarr --overwrite --compression zlib\n", + "#!./bioformats2raw-0.9.4/bin/bioformats2raw htan_wustl/HTA12_11/2.25.66963730400918147916879305140687405342/SM_1.3.6.1.4.1.5962.99.1.1999040126.632533787.1655561481854.4.0/8def879c-e010-4abf-b0d7-82893142232f.dcm htan_wustl/output.zarr --overwrite\n", + "!./raw2ometiff-0.7.1/bin/raw2ometiff htan_wustl/output.zarr htan_wustl/output-default.ome.tiff\n" ] }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": { "id": "CQ4rd17GFiKi" }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "2024-06-06 16:40:12,490 [main] WARN c.g.bioformats2raw.Converter - Non-default tile size: 512 x 512. This may cause performance issues in some applications.\n", - "2024-06-06 16:40:12,781 [main] WARN c.g.bioformats2raw.Converter - Overwriting output path rgb-dicom/output.zarr\n", - "WARNING: An illegal reflective access operation has occurred\n", - "WARNING: Illegal reflective access by com.esotericsoftware.reflectasm.AccessClassLoader (file:/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/bioformats2raw-0.9.3/lib/reflectasm-1.11.9.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)\n", - "WARNING: Please consider reporting this to the maintainers of com.esotericsoftware.reflectasm.AccessClassLoader\n", - "WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations\n", - "WARNING: All illegal access operations will be denied in a future release\n" - ] - } - ], + "outputs": [], "source": [ "# Convert DICOM to OME-TIFF with bioformats2raw/raw2ometiff with specification of compression, tile size, etc.\n", "# The '--rgb' and '--compression \"JPEG-2000\"' options to raw2ometiff should produce a file that is much smaller than\n", "# with default options.\n", "\n", - "!./bioformats2raw-0.9.3/bin/bioformats2raw rgb-dicom/5ee2770f-b222-4565-a3bd-46ba294ca222.dcm rgb-dicom/output.zarr --tile_width 512 --tile_height 512 --overwrite\n", - "#!./bioformats2raw-0.9.3/bin/bioformats2raw rgb-dicom/5ee2770f-b222-4565-a3bd-46ba294ca222.dcm rgb-dicom/output.zarr --tile_width 512 --tile_height 512 --overwrite --compression zlib\n", - "!./raw2ometiff-0.7.1/bin/raw2ometiff rgb-dicom/output.zarr rgb-dicom/output-options.ome.tiff --rgb --compression \"JPEG-2000\"\n" + "!./bioformats2raw-0.9.4/bin/bioformats2raw htan_wustl/HTA12_11/2.25.66963730400918147916879305140687405342/SM_1.3.6.1.4.1.5962.99.1.1999040126.632533787.1655561481854.4.0/8def879c-e010-4abf-b0d7-82893142232f.dcm htan_wustl/output.zarr --tile_width 512 --tile_height 512 --overwrite --compression zlib\n", + "#!./bioformats2raw-0.9.4/bin/bioformats2raw htan_wustl/HTA12_11/2.25.66963730400918147916879305140687405342/SM_1.3.6.1.4.1.5962.99.1.1999040126.632533787.1655561481854.4.0/8def879c-e010-4abf-b0d7-82893142232f.dcm htan_wustl/output.zarr --tile_width 512 --tile_height 512 --overwrite\n", + "!./raw2ometiff-0.7.1/bin/raw2ometiff htan_wustl/output.zarr htan_wustl/output-options.ome.tiff --rgb --compression \"JPEG-2000\"\n" ] }, { @@ -701,7 +283,7 @@ }, { "cell_type": "code", - 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"cp s3://idc-open-data/8b69f25f-8e90-4410-9b07-05a3d0be086b/555cdebe-b785-410f-9f7d-063a9b188dd9.dcm fluo/555cdebe-b785-410f-9f7d-063a9b188dd9.dcm\n", - "cp s3://idc-open-data/8b69f25f-8e90-4410-9b07-05a3d0be086b/b38f5ba7-df35-4f75-80ae-21ad1aef52c7.dcm fluo/b38f5ba7-df35-4f75-80ae-21ad1aef52c7.dcm\n", - "cp s3://idc-open-data/8b69f25f-8e90-4410-9b07-05a3d0be086b/9f94a226-7f6f-42fc-9323-d85b8ab3f303.dcm fluo/9f94a226-7f6f-42fc-9323-d85b8ab3f303.dcm\n", - "cp s3://idc-open-data/8b69f25f-8e90-4410-9b07-05a3d0be086b/d9b311d7-fcc1-4df2-8632-6f56dc747d9c.dcm fluo/d9b311d7-fcc1-4df2-8632-6f56dc747d9c.dcm\n", - "cp s3://idc-open-data/8b69f25f-8e90-4410-9b07-05a3d0be086b/cefdc68b-1f3b-4e0c-bbe9-0168cd838bf7.dcm fluo/cefdc68b-1f3b-4e0c-bbe9-0168cd838bf7.dcm\n", - "cp s3://idc-open-data/8b69f25f-8e90-4410-9b07-05a3d0be086b/e936af92-17e8-4833-afa7-0160ededc9af.dcm fluo/e936af92-17e8-4833-afa7-0160ededc9af.dcm\n", - "cp s3://idc-open-data/8b69f25f-8e90-4410-9b07-05a3d0be086b/49d3096b-2110-4f28-b4e8-d9a158b07dc0.dcm fluo/49d3096b-2110-4f28-b4e8-d9a158b07dc0.dcm\n", - "cp s3://idc-open-data/8b69f25f-8e90-4410-9b07-05a3d0be086b/f7fed629-5e91-491d-be77-5c59b0c321e0.dcm fluo/f7fed629-5e91-491d-be77-5c59b0c321e0.dcm\n", - "cp s3://idc-open-data/8b69f25f-8e90-4410-9b07-05a3d0be086b/bebcc3fe-6c9e-4f8a-a683-9c7d9040984b.dcm fluo/bebcc3fe-6c9e-4f8a-a683-9c7d9040984b.dcm\n", - "cp s3://idc-open-data/8b69f25f-8e90-4410-9b07-05a3d0be086b/d01294ec-c175-4d57-9b3f-5f5a9b2ca7e5.dcm fluo/d01294ec-c175-4d57-9b3f-5f5a9b2ca7e5.dcm\n", - "cp s3://idc-open-data/8b69f25f-8e90-4410-9b07-05a3d0be086b/1f3165bd-8499-4853-bc36-6a46462ee061.dcm fluo/1f3165bd-8499-4853-bc36-6a46462ee061.dcm\n" - ] - } - ], + "outputs": [], "source": [ "# Download sample fluorescence data from IDC\n", "\n", - "!s5cmd --no-sign-request --endpoint-url https://s3.amazonaws.com cp \"s3://idc-open-data/8b69f25f-8e90-4410-9b07-05a3d0be086b/*\" fluo\n" + "!idc download 1.3.6.1.4.1.5962.99.1.1997718038.181734674.1655560159766.4.0\n" ] }, { @@ -804,7 +307,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": { "colab": { "base_uri": "https://localhost:8080/" @@ -812,809 +315,16 @@ "id": "seOZBDwl3RKG", "outputId": "5f8a5094-2b33-40e5-f54e-39264fcc7bd4" }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Checking file format [DICOM]\n", - "Initializing reader\n", - "DicomReader initializing fluo/5f1c1b2e-60d4-4fae-a783-5b029ebd6db0.dcm\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Initialization took 0.242s\n", - "\n", - "Reading core metadata\n", - 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"\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/8aee2836-cc0c-4039-babe-b8e1f1e962d2.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/de59a79f-c010-4122-993c-cd5321e82866.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/27d029d8-bba6-4808-94bf-65fa155b6542.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/c9203911-2a32-46cc-a810-68d8898ff15b.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/aa4cfce2-7228-49f8-9dc6-eb51ddf11d73.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/01d18476-110f-4faf-bdef-63a4f2dcd378.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/4ed13c70-1ee7-4053-9846-8000f373a79c.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/261ba9cc-d933-4c8e-9ba6-172845b92ed8.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/6d3c097c-97d9-4826-96a9-bb6201c8e87c.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/e8af8bd8-0e0c-451f-b687-b7927f558109.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/f80c7de0-5abc-4d3c-8e1f-3ae65821fdd9.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/bb2f63a9-dcd3-46e4-b3c9-9dc597f54a3d.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/51ce1545-3a1b-443f-973a-781f253c7b42.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/d7416371-5ec6-48cc-81a0-ffae99abff43.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/360845d0-00e3-4952-9956-be7e52d83573.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/72e06dc5-94bb-4405-8d5e-2b284eb7af83.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/e108db37-8538-45fa-a05f-3b32c4904628.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/cbd2eba3-a536-4922-ae8f-61f81b9e0762.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/a80497df-cb8c-45a1-853b-66fc25756071.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/14999e10-9969-459c-b69e-9213ea540363.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/11382323-49f7-428b-8a14-cc43782240e3.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/86a87bbd-30db-4d31-9729-909a84537f40.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/f7d6e73b-6cb7-4e10-9c04-cb1389d4423b.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/2fb08a0a-19e1-4de1-8e42-bdcefcde41ff.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/3392794a-3ddf-48c1-9098-c35062f5b9aa.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/02d9484f-8a9c-4858-9f03-6825103c836f.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/a738f059-fa18-4757-b032-a06ae9f11396.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/104eee79-18f8-46d4-bbff-c498a7cd7734.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/7fee657c-dcc3-401c-a62f-0caa38a775a8.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/13eaf1e9-6c54-4579-92b4-f2f084ea490e.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/bb977bcf-dbda-4ec5-962f-1bf0a59ce448.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/5f4e569a-bbd2-4265-acb9-2e332c109790.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/ac38ac3e-01c4-4f27-be1b-1eb651f9ce15.dcm\n", - "\t/Users/erindiel/IDC-Tutorials/notebooks/advanced_topics/fluo/d18bdabd-9ee9-4d21-b18a-ac57801fc60b.dcm\n", - "Series count = 1\n", - "Series #0 :\n", - "\tResolutions = 6\n", - "\t\tsizeX[0] = 5001\n", - "\t\tsizeX[1] = 2500\n", - "\t\tsizeX[2] = 1250\n", - "\t\tsizeX[3] = 625\n", - "\t\tsizeX[4] = 312\n", - "\t\tsizeX[5] = 156\n", - "\tImage count = 12\n", - "\tRGB = false (1) \n", - "\tInterleaved = false\n", - "\tIndexed = false (true color)\n", - "\tWidth = 5001\n", - "\tHeight = 5001\n", - "\tSizeZ = 1\n", - "\tSizeT = 1\n", - "\tSizeC = 12\n", - "\tTile size = 1024 x 1024\n", - "\tThumbnail size = 128 x 128\n", - "\tEndianness = intel (little)\n", - "\tDimension order = XYCZT (certain)\n", - "\tPixel type = uint8\n", - "\tValid bits per pixel = 8\n", - "\tMetadata complete = true\n", - "\tThumbnail series = false\n", - "\t-----\n", - "\tPlane #0 <=> Z 0, C 0, T 0\n", - "\tPlane #4 <=> Z 0, C 4, T 0\n", - "\tPlane #5 <=> Z 0, C 5, T 0\n", - "\tPlane #6 <=> Z 0, C 6, T 0\n", - "\tPlane #7 <=> Z 0, C 7, T 0\n", - "\tPlane #8 <=> Z 0, C 8, T 0\n", - "\tPlane #11 <=> Z 0, C 11, T 0\n", - "\n", - "\n", - "Reading global metadata\n", - "\n", - "Reading metadata\n", - "0002,0000 File Meta Information Group Length: 222\n", - "0002,0002 Media Storage SOP Class UID: 1.2.840.10008.5.1.4.1.1.77.1.6\n", - "0002,0003 Media Storage SOP Instance UID: 1.3.6.1.4.1.5962.99.1.1999932010.1115442694.1655562373738.10.0\n", - "0002,0010 Transfer Syntax UID: 1.2.840.10008.1.2.1\n", - "0002,0012 Implementation Class UID: 1.3.6.1.4.1.5962.99.2\n", - "0002,0013 Implementation Version Name: PIXELMEDJAVA001\n", - "0002,0016 Source Application Entity Title: OURAETITLE\n", - "0008,0008 Image Type: DERIVED\\PRIMARY\\VOLUME\\NONE\n", - "0008,0012 Instance Creation Date: 20220618\n", - "0008,0013 Instance Creation Time: 142615.237\n", - "0008,0014 Instance Creator UID: 1.3.6.1.4.1.5962.99.3\n", - "0008,0016 SOP Class UID: 1.2.840.10008.5.1.4.1.1.77.1.6\n", - "0008,0017: 1.3.6.1.4.1.5962.99.1.1999932010.1115442694.1655562373738.3.0\n", - "0008,0018 SOP Instance UID: 1.3.6.1.4.1.5962.99.1.1999932010.1115442694.1655562373738.10.0\n", - "0008,0019: 1.3.6.1.4.1.5962.99.1.1999932010.1115442694.1655562373738.2.0\n", - "0008,0020 Study Date: 20220618\n", - "0008,0021 Series Date: 20220618\n", - "0008,0022 Acquisition Date: 20220618\n", - "0008,0023 Content Date: 20220618\n", - "0008,002a Acquisition Date/Time: 20220618142613.834\n", - "0008,0030 Study Time: 142613.834\n", - "0008,0031 Series Time: 142613.834\n", - "0008,0032 Acquisition Time: 142613.834\n", - "0008,0033 Content Time: 142613.834\n", - "0008,0050 Accession Number: HTA9_1\n", - "0008,0060 Modality: SM\n", - "0008,0070 Manufacturer #1: Leica Biosystems\n", - "0008,0070 Manufacturer #2: PixelMed\n", - "0008,0080 Institution Name #1: Oregon Health Sciences University\n", - "0008,0080 Institution Name #2: PixelMed\n", - "0008,0081 Institution Address: Bangor, PA\n", - "0008,0090 Referring Physician's Name: ^^^^\n", - "0008,0100 Code Value #01: 109103\n", - "0008,0100 Code Value #02: 433466003\n", - "0008,0100 Code Value #03: 11323-3\n", - "0008,0100 Code Value #04: 438949009\n", - "0008,0100 Code Value #05: 10200004\n", - "0008,0100 Code Value #06: 14799000\n", - "0008,0100 Code Value #07: 121041\n", - "0008,0100 Code Value #08: 111701\n", - "0008,0100 Code Value #09: 17636008\n", - "0008,0100 Code Value #10: 17636008\n", - "0008,0100 Code Value #11: 86273004\n", - "0008,0100 Code Value #12: 121041\n", - "0008,0100 Code Value #13: 434711009\n", - "0008,0100 Code Value #14: 433466003\n", - "0008,0100 Code Value #15: 371439000\n", - "0008,0100 Code Value #16: 1179252003\n", - "0008,0100 Code Value #17: 111701\n", - "0008,0100 Code Value #18: 433465004\n", - "0008,0100 Code Value #19: 111704\n", - "0008,0100 Code Value #20: 434472006\n", - "0008,0100 Code Value #21: 111705\n", - "0008,0100 Code Value #22: 111707\n", - "0008,0100 Code Value #23: 430861001\n", - "0008,0100 Code Value #24: 121041\n", - "0008,0100 Code Value #25: 111701\n", - "0008,0100 Code Value #26: 127790008\n", - "0008,0100 Code Value #27: C44170\n", - "0008,0100 Code Value #28: C25472\n", - "0008,0100 Code Value #29: 313001\n", - "0008,0100 Code Value #30: 246094008\n", - "0008,0100 Code Value #31: 84640000\n", - "0008,0100 Code Value #32: 246094008\n", - "0008,0100 Code Value #33: C2480\n", - "0008,0100 Code Value #34: C0598447\n", - "0008,0100 Code Value #35: 424361007\n", - "0008,0100 Code Value #36: 12710003\n", - "0008,0100 Code Value #37: 424361007\n", - "0008,0100 Code Value #38: 703857004\n", - "0008,0100 Code Value #39: 406858009\n", - "0008,0100 Code Value #40: C37925\n", - "0008,0100 Code Value #41: C0947322\n", - "0008,0100 Code Value #42: 111529\n", - "0008,0100 Code Value #43: 111743\n", - "0008,0100 Code Value #44: 134223000\n", - "0008,0102 Coding Scheme Designator #01: 99PMP\n", - "0008,0102 Coding Scheme Designator #02: DCM\n", - "0008,0102 Coding Scheme Designator #03: LN\n", - "0008,0102 Coding Scheme Designator #04: NCIt\n", - "0008,0102 Coding Scheme Designator #05: SCT\n", - "0008,0102 Coding Scheme Designator #06: UMLS\n", - "0008,0102 Coding Scheme Designator #07: DCM\n", - "0008,0102 Coding Scheme Designator #08: SCT\n", - "0008,0102 Coding Scheme Designator #09: LN\n", - "0008,0102 Coding Scheme Designator #10: SCT\n", - "0008,0102 Coding Scheme Designator #11: SCT\n", - "0008,0102 Coding Scheme Designator #12: SCT\n", - "0008,0102 Coding Scheme Designator #13: DCM\n", - "0008,0102 Coding Scheme Designator #14: DCM\n", - "0008,0102 Coding Scheme Designator #15: SCT\n", - "0008,0102 Coding Scheme Designator #16: SCT\n", - "0008,0102 Coding Scheme Designator #17: SCT\n", - "0008,0102 Coding Scheme Designator #18: DCM\n", - "0008,0102 Coding Scheme Designator #19: SCT\n", - "0008,0102 Coding Scheme Designator #20: SCT\n", - "0008,0102 Coding Scheme Designator #21: SCT\n", - "0008,0102 Coding Scheme Designator #22: SCT\n", - "0008,0102 Coding Scheme Designator #23: DCM\n", - "0008,0102 Coding Scheme Designator #24: SCT\n", - "0008,0102 Coding Scheme Designator #25: DCM\n", - "0008,0102 Coding Scheme Designator #26: SCT\n", - "0008,0102 Coding Scheme Designator #27: DCM\n", - "0008,0102 Coding Scheme Designator #28: DCM\n", - "0008,0102 Coding Scheme Designator #29: SCT\n", - "0008,0102 Coding Scheme Designator #30: DCM\n", - "0008,0102 Coding Scheme Designator #31: DCM\n", - "0008,0102 Coding Scheme Designator #32: SCT\n", - "0008,0102 Coding Scheme Designator #33: NCIt\n", - "0008,0102 Coding Scheme Designator #34: NCIt\n", - "0008,0102 Coding Scheme Designator #35: 99PMP\n", - "0008,0102 Coding Scheme Designator #36: SCT\n", - "0008,0102 Coding Scheme Designator #37: SCT\n", - "0008,0102 Coding Scheme Designator #38: SCT\n", - "0008,0102 Coding Scheme Designator #39: NCIt\n", - "0008,0102 Coding Scheme Designator #40: UMLS\n", - "0008,0102 Coding Scheme Designator #41: SCT\n", - "0008,0102 Coding Scheme Designator #42: SCT\n", - "0008,0102 Coding Scheme Designator #43: SCT\n", - "0008,0102 Coding Scheme Designator #44: SCT\n", - "0008,0102 Coding Scheme Designator #45: SCT\n", - "0008,0102 Coding Scheme Designator #46: NCIt\n", - "0008,0102 Coding Scheme Designator #47: UMLS\n", - "0008,0102 Coding Scheme Designator #48: DCM\n", - "0008,0102 Coding Scheme Designator #49: DCM\n", - "0008,0102 Coding Scheme Designator #50: SCT\n", - "0008,0104 Code Meaning #01: Modifying Equipment\n", - "0008,0104 Code Meaning #02: Microscope slide\n", - "0008,0104 Code Meaning #03: Health status\n", - "0008,0104 Code Meaning #04: Alive\n", - "0008,0104 Code Meaning #05: Liver\n", - "0008,0104 Code Meaning #06: Neoplasm, Metastatic\n", - "0008,0104 Code Meaning #07: Specimen Identifier\n", - "0008,0104 Code Meaning #08: Processing type\n", - "0008,0104 Code Meaning #09: Specimen Collection\n", - "0008,0104 Code Meaning #10: Specimen Collection\n", - "0008,0104 Code Meaning #11: Biopsy\n", - "0008,0104 Code Meaning #12: Specimen Identifier\n", - "0008,0104 Code Meaning #13: Specimen container\n", - "0008,0104 Code Meaning #14: Microscope slide\n", - "0008,0104 Code Meaning #15: Specimen type\n", - "0008,0104 Code Meaning #16: Slide\n", - "0008,0104 Code Meaning #17: Processing type\n", - "0008,0104 Code Meaning #18: Specimen Sampling\n", - "0008,0104 Code Meaning #19: Sampling Method\n", - "0008,0104 Code Meaning #20: Block sectioning\n", - "0008,0104 Code Meaning #21: Parent Specimen Identifier\n", - "0008,0104 Code Meaning #22: Parent specimen type\n", - "0008,0104 Code Meaning #23: Gross specimen\n", - "0008,0104 Code Meaning #24: Specimen Identifier\n", - "0008,0104 Code Meaning #25: Processing type\n", - "0008,0104 Code Meaning #26: Staining\n", - "0008,0104 Code Meaning #27: Channel\n", - "0008,0104 Code Meaning #28: Cycle\n", - "0008,0104 Code Meaning #29: Subcycle\n", - "0008,0104 Code Meaning #30: Component investigated\n", - "0008,0104 Code Meaning #31: Nucleus\n", - "0008,0104 Code Meaning #32: Component investigated\n", - "0008,0104 Code Meaning #33: Tracer\n", - "0008,0104 Code Meaning #34: Fluorophore\n", - "0008,0104 Code Meaning #35: Using substance\n", - "0008,0104 Code Meaning #36: Hematoxylin\n", - "0008,0104 Code Meaning #37: Using substance\n", - "0008,0104 Code Meaning #38: Staining Technique\n", - "0008,0104 Code Meaning #39: Fluorescent staining\n", - "0008,0104 Code Meaning #40: Clone\n", - "0008,0104 Code Meaning #41: Manufacturer Name\n", - "0008,0104 Code Meaning #42: Brand Name\n", - "0008,0104 Code Meaning #43: Epifluorescence illumination\n", - "0008,0104 Code Meaning #44: Narrow\n", - "0008,010c Coding Scheme UID #1: 1.3.6.1.4.1.5962.98.1\n", - "0008,010c Coding Scheme UID #2: 1.2.840.10008.2.16.4\n", - "0008,010c Coding Scheme UID #3: 2.16.840.1.113883.6.1\n", - "0008,010c Coding Scheme UID #4: 2.16.840.1.113883.3.26.1.1\n", - "0008,010c Coding Scheme UID #5: 2.16.840.1.113883.6.96\n", - "0008,010c Coding Scheme UID #6: 2.16.840.1.113883.6.86\n", - "0008,0112 Coding Scheme Registry #1: HL7\n", - "0008,0112 Coding Scheme Registry #2: HL7\n", - "0008,0112 Coding Scheme Registry #3: HL7\n", - "0008,0112 Coding Scheme Registry #4: HL7\n", - "0008,0112 Coding Scheme Registry #5: HL7\n", - "0008,0115 Coding Scheme Name #1: PixelMed Publishing\n", - "0008,0115 Coding Scheme Name #2: DICOM Controlled Terminology\n", - "0008,0115 Coding Scheme Name #3: LOINC\n", - "0008,0115 Coding Scheme Name #4: NCI Thesaurus\n", - "0008,0115 Coding Scheme Name #5: SNOMED CT using SNOMED-CT style values\n", - "0008,0115 Coding Scheme Name #6: UMLS codes as CUIs making up the values in a coding system\n", - "0008,0201 Timezone Offset from UTC: +0000\n", - "0008,103e Series Description: mIHC\n", - "0008,1040 Institutional Department Name: Software Development\n", - "0008,1090 Manufacturer's Model Name #1: Aperio AT2 converted by com.pixelmed.convert.TIFFToDicom\n", - "0008,1090 Manufacturer's Model Name #2: com.pixelmed.convert.TIFFToDicom\n", - "0008,9007 Frame Type: DERIVED\\PRIMARY\\VOLUME\\NONE\n", - "0008,9206 Volumetric Properties: VOLUME\n", - "0009,0010: PixelMed Publishing\n", - "0009,1001: HTAN-OHSU/mIHC/HTA9_1_BB_F_ROI02.ome.tif\n", - "0009,1002: 0\n", - "0010,0010 Patient's Name: HTA9_1^\n", - "0010,0020 Patient ID: HTA9_1\n", - "0010,0030 Patient's Birth Date: \n", - "0010,0040 Patient's Sex: F\n", - "0010,2160 Ethnic Group: White\n", - "0012,0010 Clinical Trial Sponsor Name: NCI\n", - "0012,0020 Clinical Trial Protocol ID: HTAN-OHSU\n", - "0012,0021 Clinical Trial Protocol Name: \n", - "0012,0030 Clinical Trial Site ID: HTAN-OHSU\n", - "0012,0031 Clinical Trial Site Name: Oregon Health Sciences University\n", - "0012,0040 Clinical Trial Subject ID: HTA9_1\n", - "0012,0050 Clinical Trial Time Point ID: Biopsy 1\n", - "0012,0060 Clinical Trial Coordinating Center Name: HTAN\n", - "0013,0010: CTP\n", - "0013,1010: HTAN-OHSU\n", - "0018,0050 Slice Thickness: 0\n", - "0018,1000 Device Serial Number: 5b2498543e593b08:427c4e06:18177350a6a:-7ff3\n", - "0018,1020 Software Version(s) #1: Sat Jun 18 09:29:28 EDT 2022\n", - "0018,1020 Software Version(s) #2: Vers. Sat Jun 18 09:29:28 EDT 2022\n", - "0018,9004 Content Qualification: RESEARCH\n", - "0018,a002 Contribution DateTime: 20220618142615.247+0000\n", - "0018,a003 Contribution Description: TIFF to DICOM conversion\n", - "0020,000d Study Instance UID: 2.25.56219147941526607962658668060030231728\n", - "0020,000e Series Instance UID: 1.3.6.1.4.1.5962.99.1.1999932010.1115442694.1655562373738.4.0\n", - "0020,0010 Study ID: HTA9_1\n", - "0020,0011 Series Number: 1\n", - "0020,0013 Instance Number: 1\n", - "0020,0020 Patient Orientation: \n", - "0020,0052 Frame of Reference UID: 1.3.6.1.4.1.5962.99.1.1999932010.1115442694.1655562373738.7.0\n", - "0020,1040 Position Reference Indicator: UNKNOWN\n", - "0020,9164 Dimension Organization UID #1: 1.3.6.1.4.1.5962.99.1.1999932010.1115442694.1655562373738.15.0\n", - "0020,9164 Dimension Organization UID #2: 1.3.6.1.4.1.5962.99.1.1999932010.1115442694.1655562373738.15.0\n", - "0020,9164 Dimension Organization UID #3: 1.3.6.1.4.1.5962.99.1.1999932010.1115442694.1655562373738.15.0\n", - "0020,9311 Dimension Organization Type: TILED_FULL\n", - "0020,9421 Dimension Description Label #1: Row Position\n", - "0020,9421 Dimension Description Label #2: Column Position\n", - "0028,0002 Samples per pixel: 1\n", - "0028,0004 Photometric Interpretation: MONOCHROME2\n", - "0028,0008 Number of frames: 25\n", - "0028,0010 Rows: 1024\n", - "0028,0011 Columns: 1024\n", - "0028,0030 Pixel Spacing: .0005022\\.0005022\n", - "0028,0100 Bits Allocated: 8\n", - "0028,0101 Bits Stored: 8\n", - "0028,0102 High Bit: 7\n", - "0028,0103 Pixel Representation: 0\n", - "0028,0301 Burned in Annotation: NO\n", - "0028,0302 Recognizable Visual Features: NO\n", - "0028,1052 Rescale Intercept: 0\n", - "0028,1053 Rescale Slope: 1\n", - "0028,2110 Lossy Image Compression: 00\n", - "0040,0512 Container Identifier: HTA9_1_19375\n", - "0040,0551 Specimen Identifier: HTA9_1_19375\n", - "0040,0554 Specimen UID: 2.25.198606588993547821018125112095302541747\n", - "0040,0600 Specimen Short Description: mIHC\n", - "0040,072a X Offset in Slide Coordinate System: 0\n", - "0040,073a Y Offset in Slide Coordinate System: 0\n", - "0040,a040 Value Type #01: CODE\n", - "0040,a040 Value Type #02: TEXT\n", - "0040,a040 Value Type #03: CODE\n", - "0040,a040 Value Type #04: CODE\n", - "0040,a040 Value Type #05: TEXT\n", - "0040,a040 Value Type #06: CODE\n", - "0040,a040 Value Type #07: CODE\n", - "0040,a040 Value Type #08: CODE\n", - "0040,a040 Value Type #09: CODE\n", - "0040,a040 Value Type #10: TEXT\n", - "0040,a040 Value Type #11: CODE\n", - "0040,a040 Value Type #12: TEXT\n", - "0040,a040 Value Type #13: CODE\n", - "0040,a040 Value Type #14: TEXT\n", - "0040,a040 Value Type #15: TEXT\n", - "0040,a040 Value Type #16: TEXT\n", - "0040,a040 Value Type #17: CODE\n", - "0040,a040 Value Type #18: TEXT\n", - "0040,a040 Value Type #19: CODE\n", - "0040,a040 Value Type #20: CODE\n", - "0040,a040 Value Type #21: TEXT\n", - "0040,a040 Value Type #22: CODE\n", - "0040,a040 Value Type #23: TEXT\n", - "0040,a040 Value Type #24: TEXT\n", - "0040,a040 Value Type #25: TEXT\n", - "0040,a160 Text Value #01: HTA9_1_31\n", - "0040,a160 Text Value #02: HTA9_1_19375\n", - "0040,a160 Text Value #03: HTA9_1_31\n", - "0040,a160 Text Value #04: HTA9_1_19375\n", - "0040,a160 Text Value #05: 0\n", - "0040,a160 Text Value #06: 01\n", - "0040,a160 Text Value #07: 01\n", - "0040,a160 Text Value #08: NUCLEI\n", - "0040,a160 Text Value #09: hematoxylin\n", - "0040,a160 Text Value #10: NA\n", - "0040,a160 Text Value #11: Dako\n", - "0040,a160 Text Value #12: S330130-2\n", - "0048,0001 Imaged Volume Width (mm): 2.5115023\n", - "0048,0002 Imaged Volume Height (mm): 2.5115023\n", - "0048,0003 Imaged Volume Depth (mm): 0.0\n", - "0048,0006 Total Pixel Matrix Columns: 5001\n", - "0048,0007 Total Pixel Matrix Rows: 5001\n", - "0048,0010 Specimen Label in Image: NO\n", - "0048,0011 Focus Method: AUTO\n", - "0048,0012 Extended Depth of Field: NO\n", - "0048,0102 Image Orientation (Slide): 0\\-1\\0\\-1\\0\\0\n", - "0048,0106 Optical Path Identifier: 0\n", - "0048,0107 Optical Path Description: NUCLEI\n", - "0048,0112 Objective Lens Power: 20\n", - "0048,0113 Objective Lens Numerical Aperture: 0.75\n", - "0048,0302 Number of Optical Paths: 1\n", - "0048,0303 Total Pixel Matrix Focal Planes: 1\n", - "2050,0020 Presentation LUT Shape: IDENTITY\n" - ] - } - ], + "outputs": [], "source": [ "# Use bftools to describe this fluorescence dataset\n", "\n", - "!./bftools/showinf -nopix -noflat fluo/5f1c1b2e-60d4-4fae-a783-5b029ebd6db0.dcm\n" + "!./bftools/showinf -nopix -noflat htan_wustl/HTA12_11/2.25.66963730400918147916879305140687405342/SM_1.3.6.1.4.1.5962.99.1.1997718038.181734674.1655560159766.4.0/5fc84bfa-a1e0-4b37-bc81-721b8b1ab3a6.dcm\n" ] }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": { "colab": { "base_uri": "https://localhost:8080/" @@ -1622,385 +332,7 @@ "id": "jFOl78-cz6Xp", "outputId": "8452e5d5-eee4-4a32-b7a5-4e3d2a2a1346" }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "fluo/5f1c1b2e-60d4-4fae-a783-5b029ebd6db0.dcm\n", - "DicomReader initializing fluo/5f1c1b2e-60d4-4fae-a783-5b029ebd6db0.dcm\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "Verifying DICOM format\n", - "Reading tags\n", - "Calculating image offsets\n", - "Building file list\n", - "Populating metadata\n", - "[DICOM] -> fluo/fluo-cropped.ome.tiff [OME-TIFF]\n", - "\tSeries 0: converted 12/12 planes (100%)\n", - "\tSeries 1: converted 12/12 planes (100%)\n", - "\tSeries 2: converted 12/12 planes (100%)\n", - "\tSeries 3: converted 12/12 planes (100%)\n", - "\tSeries 4: converted 12/12 planes (100%)\n", - "\tSeries 5: converted 12/12 planes (100%)\n", - "[done]\n", - "1.185s elapsed (0.6666667+6.263889ms per plane, 567ms overhead)\n" - ] - } - ], + "outputs": [], "source": [ "# Convert fluoresence data using bfconvert - cropping a subset due to its size\n", "# A 1000x1000 region of the full resolution image starting at (0,0) is saved.\n", @@ -2010,7 +342,7 @@ "# - omit the '-crop 0,0,1000,1000' option\n", "# - replace the '-series 0' option with '-noflat'\n", "\n", - "!./bftools/bfconvert -series 0 -crop 0,0,1000,1000 fluo/5f1c1b2e-60d4-4fae-a783-5b029ebd6db0.dcm fluo/fluo-cropped.ome.tiff\n" + "!./bftools/bfconvert -series 0 -crop 0,0,1000,1000 htan_wustl/HTA12_11/2.25.66963730400918147916879305140687405342/SM_1.3.6.1.4.1.5962.99.1.1997718038.181734674.1655560159766.4.0/5fc84bfa-a1e0-4b37-bc81-721b8b1ab3a6.dcm htan_wustl/fluo.ome.tiff\n" ] }, { @@ -2056,7 +388,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.14" + "version": "3.10.15" } }, "nbformat": 4, From d03103b09a2564c2fac235ef4040ca513376284a Mon Sep 17 00:00:00 2001 From: erindiel Date: Tue, 22 Oct 2024 17:20:11 -0400 Subject: [PATCH 2/3] clarify compression option --- notebooks/advanced_topics/IDC_Recipes_Conversion.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/notebooks/advanced_topics/IDC_Recipes_Conversion.ipynb b/notebooks/advanced_topics/IDC_Recipes_Conversion.ipynb index 272804b..d15a763 100644 --- a/notebooks/advanced_topics/IDC_Recipes_Conversion.ipynb +++ b/notebooks/advanced_topics/IDC_Recipes_Conversion.ipynb @@ -202,7 +202,7 @@ "\n", "# TIP: If conversion fails with \"java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll\"\n", "# Follow instructions here for Blosc installation: https://github.com/glencoesoftware/bioformats2raw/?tab=readme-ov-file#requirements\n", - "# OR add \"--compression zlib\" to the \"bioformats2raw\" command below\n", + "# OR add \"--compression zlib\" as in the first \"bioformats2raw\" command below\n", "\n", "# Use a single .dcm file as input\n", "\n", From eba75b633eb3dcf157160586a7fe219e366a8047 Mon Sep 17 00:00:00 2001 From: erindiel Date: Fri, 25 Oct 2024 14:45:26 -0400 Subject: [PATCH 3/3] use bio-formats 8.0.0 for precompressed option --- notebooks/advanced_topics/IDC_Recipes_Conversion.ipynb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/notebooks/advanced_topics/IDC_Recipes_Conversion.ipynb b/notebooks/advanced_topics/IDC_Recipes_Conversion.ipynb index d15a763..d1c1a1d 100644 --- a/notebooks/advanced_topics/IDC_Recipes_Conversion.ipynb +++ b/notebooks/advanced_topics/IDC_Recipes_Conversion.ipynb @@ -47,7 +47,7 @@ "!pip install idc-index\n", "\n", "# Install bfconvert via bftools\n", - "!wget https://downloads.openmicroscopy.org/bio-formats/latest/artifacts/bftools.zip\n", + "!wget https://downloads.openmicroscopy.org/bio-formats/8.0.0/artifacts/bftools.zip\n", "!unzip bftools.zip\n" ] }, @@ -104,14 +104,11 @@ }, "outputs": [], "source": [ - "# Convert SVS to DICOM with precompressed tiles\n", + "# Convert SVS to DICOM with precompressed tiles using \"-precompressed\"\n", "# This will copy tiles from the original SVS, so tile sizes do not need to be specified\n", "\n", - "# The '-compression' option currently must match the compression type of the input data.\n", - "# This will be fixed in a future version of Bio-Formats.\n", - "\n", "# Convert using bfconvert\n", - "!./bftools/bfconvert -noflat -precompressed -compression JPEG -overwrite rgb-svs/CMU-1-Small-Region.svs rgb-svs/CMU-1-Small-Region.dcm\n" + "!./bftools/bfconvert -noflat -precompressed -overwrite rgb-svs/CMU-1-Small-Region.svs rgb-svs/CMU-1-Small-Region.dcm\n" ] }, {