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Jun 17, 2024
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Typo fixes, expand a few comments #1

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29 changes: 25 additions & 4 deletions notebooks/advanced_topics/IDC_Recipes_Conversion.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@
"source": [
"### Sample data for conversion examples\n",
"\n",
"Expore and download IDC data here: https://portal.imaging.datacommons.cancer.gov/explore/\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",
Expand Down Expand Up @@ -218,9 +218,13 @@
],
"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",
"\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 -precompressed -compression JPEG -overwrite rgb-svs/CMU-1-Small-Region.svs rgb-svs/CMU-1-Small-Region.dcm\n"
"!./bftools/bfconvert -noflat -precompressed -compression JPEG -overwrite rgb-svs/CMU-1-Small-Region.svs rgb-svs/CMU-1-Small-Region.dcm\n"
]
},
{
Expand Down Expand Up @@ -278,6 +282,14 @@
"\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",
"\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"
]
Expand Down Expand Up @@ -592,6 +604,7 @@
],
"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",
"\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",
Expand Down Expand Up @@ -625,10 +638,12 @@
],
"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/raw2ometiffraw2ometiff rgb-dicom/output.zarr rgb-dicom/output-options.ome.tiff -rgb --compression \"JPEG-2000\"\n"
"!./raw2ometiff-0.7.1/bin/raw2ometiff rgb-dicom/output.zarr rgb-dicom/output-options.ome.tiff --rgb --compression \"JPEG-2000\"\n"
]
},
{
Expand Down Expand Up @@ -1988,8 +2003,14 @@
],
"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",
"# The pyramid is omitted due to the small output image size.\n",
"\n",
"# If converting the entire input dataset instead:\n",
"# - omit the '-crop 0,0,1000,1000' option\n",
"# - replace the '-series 0' option with '-noflat'\n",
"\n",
"!./bftools/bfconvert -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 fluo/5f1c1b2e-60d4-4fae-a783-5b029ebd6db0.dcm fluo/fluo-cropped.ome.tiff\n"
]
},
{
Expand Down