Wolfram Language Paclet Repository
Community-contributed installable additions to the Wolfram Language
Images Download
The TCGA Data Tool user interface allows easy retrieval of data for the TCGA projects from GDC and TCIA portals. Data categories such as ScrapedData::HistologicalImages or ScrapedData::RadiologicalImages do not contain actual patient images but only their metadata. Histological images can be downloaded using separate paclet functionalities, while radiological images can be downloaded from the dedicated user interface pane.
This loads the paclet.
In[1]:=
Needs["JaneShenGunther`TCGADataTool`"]
Histological images
getHistologicalImages | download all histological images for patientUUID |
Get example data structure for project TCGA-CESC. Then select a valid patient UUID from that data structure.
In[2]:=
dataStructure=
[{"TCGAProjectData","TCGACESCExceptGenomicDataAllPatients"}];
 | exampleDataTCGA |
In[3]:=
examplePatientUUID="03804F9B-DF7C-462C-8984-8EB3A5ED4999";
Download all histological images for the selected patient UUID.
In[4]:=
 | getHistologicalImages |
Mon 27 Feb 2023 14:34:18 Getting histological images for patient UUID 03804F9B-DF7C-462C-8984-8EB3A5ED4999...
Mon 27 Feb 2023 14:34:18 Identified 2 histological images for patient UUID 03804F9B-DF7C-462C-8984-8EB3A5ED4999
Mon 27 Feb 2023 14:34:18 Total histological images file size for patient UUID 03804F9B-DF7C-462C-8984-8EB3A5ED4999:
400.982
MB
Mon 27 Feb 2023 14:34:18 Starting download...
Mon 27 Feb 2023 14:34:18 Downloading file ID 821e284e-0846-466e-862a-3d8e80cc4b3a: file size: , file name: TCGA-VS-A9V2-01Z-00-DX1.61AD73DF-4A1D-4398-9558-00ADAF82952A.svs, file experimental strategy: Diagnostic Slide
171.884
MB
Mon 27 Feb 2023 14:35:07 Download completed successfully.
Mon 27 Feb 2023 14:35:07 Downloading file ID 89fb2c28-2eba-406c-a687-385e8ccfc468: file size: , file name: TCGA-VS-A9V2-01A-01-TS1.84BB47F0-6ECC-4C57-BBFF-7A833624E45E.svs, file experimental strategy: Tissue Slide
229.098
MB
Mon 27 Feb 2023 14:36:09 Download completed successfully.
Mon 27 Feb 2023 14:36:09 Download completed.
Out[4]=
{/private/var/folders/9s/ssw_w4pj5tsfxv3r6yrjj1mw0000gn/T/TCGADataTool/03804F9B-DF7C-462C-8984-8EB3A5ED4999/821e284e-0846-466e-862a-3d8e80cc4b3a/TCGA-VS-A9V2-01Z-00-DX1.61AD73DF-4A1D-4398-9558-00ADAF82952A.svs,/private/var/folders/9s/ssw_w4pj5tsfxv3r6yrjj1mw0000gn/T/TCGADataTool/03804F9B-DF7C-462C-8984-8EB3A5ED4999/89fb2c28-2eba-406c-a687-385e8ccfc468/TCGA-VS-A9V2-01A-01-TS1.84BB47F0-6ECC-4C57-BBFF-7A833624E45E.svs}
Radiological images
Radiological images can be downloaded and inspected from the . In addition, radiological images can be downloaded and processed in batches using the function . In general, the user interface is best suited to inspect radiological images for a small sample of patients, while the batch processing functionality aims at processing several radiological images at once in order to extract meaningful patient measurements to be included in a design matrix.
radiologicalImagesBatchProcessing patientUUID 1 | download and process radiological images |
Get example data for TCGA-CESC project and select a set of valid patient UUIDs.
In[29]:=
dataStructure=
[{"TCGAProjectData","TCGACESCExceptGenomicDataAllPatients"}];
| exampleDataTCGA |
In[79]:=
patientUUIDs={"03804f9b-df7c-462c-8984-8eb3a5ed4999"};
Define processing function to be applied to each radiological image. The function below computes percentage of white pixels in an image.
In[35]:=
ClearAll[computeWhitePercentage];computeWhitePercentage[img_Image]:=Module[{binaryImg,imgData,whitePixelsCount,pixelsCount}, binaryImg=Binarize[img]; imgData=ImageData[binaryImg]; whitePixelsCount=Count[Flatten[imgData],1]; pixelsCount=Length[Flatten[imgData]]; N[whitePixelsCount/pixelsCount]]
Batch process all images for the selected patient UUIDs. For each patient, compute the percentage of white pixels.
In[80]:=
processingResult=
[dataStructure,patientUUIDs,"DeleteDownloadedFilesAfterProcessingQ"True,"ImageProcessingFunctions"{computeWhitePercentage[#]&},"PatientImageProcessingResultsAggregationFunction"(Mean[#]&)]
 | radiologicalImagesBatchProcessing |
Mon 27 Feb 2023 18:47:36 Processing patient UUID 03804f9b-df7c-462c-8984-8eb3a5ed4999
Mon 27 Feb 2023 18:47:36 Getting radiological images for patient UUID 03804f9b-df7c-462c-8984-8eb3a5ed4999...
Mon 27 Feb 2023 18:47:36 Identified 11 radiological image series for patient UUID 03804f9b-df7c-462c-8984-8eb3a5ed4999
Mon 27 Feb 2023 18:47:36 Download for patient UUID 03804f9b-df7c-462c-8984-8eb3a5ed4999 started...
Mon 27 Feb 2023 18:47:56 Download for patient UUID 03804f9b-df7c-462c-8984-8eb3a5ed4999 completed.
Mon 27 Feb 2023 18:47:57 Starting processing of 386images...
Mon 27 Feb 2023 18:48:58 Processing of images completed.
Mon 27 Feb 2023 18:48:58 Processing results aggregation...
Mon 27 Feb 2023 18:48:58 Deleted downloaded files for patient UUID 03804f9b-df7c-462c-8984-8eb3a5ed4999
Mon 27 Feb 2023 18:48:58 Done processing for patient UUID 03804f9b-df7c-462c-8984-8eb3a5ed4999
Out[80]=
{bcr_patient_uuid03804f9b-df7c-462c-8984-8eb3a5ed4999,ImageProcessingResult0.27155}
In[81]:=
outcomeProperty="Clinical::Patient::vital_status";predictors={"Clinical::Patient::person_neoplasm_cancer_status","Clinical::Patient::eastern_cancer_oncology_group","Biospecimen::Analyte::analyte_type"};
In[94]:=
designMatrix=
[dataStructure,predictors,outcomeProperty,"GeneralListHandlingFunction"(If[ListQ[#],First[#],#]&),"AdditionalPatientInformation"processingResult,"DeleteAllSame"False];
| buildDesignMatrix |
In[95]:=
designMatrix//Length
Out[95]=
307
In[96]:=
designMatrix〚;;3〛//Dataset
Out[96]=
|
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""