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Open Imaging Index
MRI Pathology slides Brain

UPENN-GBM

University of Pennsylvania Glioblastoma Imaging, Genomics, and Radiomics

Multi-parametric brain MRI (T1, contrast-enhanced T1, T2, FLAIR, DTI, DSC) of 630 de novo glioblastoma patients from the University of Pennsylvania, with tumor sub-region segmentations, survival, IDH and MGMT data, radiomic features and a few H&E slides.

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Overview

UPENN-GBM is a single-center collection of brain MRI from 630 adults with newly diagnosed (de novo) glioblastoma, treated at the University of Pennsylvania Health System between 2006 and 2018. It was assembled by the Penn imaging group behind CaPTk and BraTS and is hosted by The Cancer Imaging Archive. Besides the scans it ships clinical, molecular and radiomic tables, which makes it a common source for tumor segmentation, survival prediction and radiogenomic studies.

Composition

There are 671 scan sessions: 611 pre-operative baseline sessions and 60 sessions acquired before a second resection for suspected progression. For 19 of those 60 patients only the follow-up session is included. Every session has native T1, contrast-enhanced T1, T2 and FLAIR; 592 sessions also have DTI and 534 have DSC perfusion. Patients are 60% male and aged 18 to 89. The clinical table gives sex, age, overall survival (452 patients), extent of resection, IDH1 status (16 mutated, 499 wildtype, 96 not otherwise specified among baseline cases), MGMT promoter methylation (317 baseline cases) and, for follow-up cases, a pathology score of tumor progression versus treatment effect. Version 2 added 71 H&E whole-slide images from 34 patients, with a mapping to the radiology IDs.

Acquisition

Scans come from routine clinical exams, mostly on Siemens 3 T systems; a minority were acquired at 1.5 T and eight sessions on GE scanners. The original DICOM series are defaced. A NIfTI release is also provided in which all structural scans are rigidly registered to the SRI atlas, resampled to 1 mm isotropic voxels and skull-stripped, together with DTI maps (trace, axial and radial diffusivity, fractional anisotropy) and DSC maps (peak height, percentage signal recovery, an rCBV proxy).

Annotations

Enhancing tumor, necrotic core and peritumoral edema were segmented on every baseline session by fusing three BraTS-ranked networks with STAPLE. For 232 subjects the labels were reviewed and corrected by two experts. CaPTk radiomic features (145 per sub-region and sequence) are provided for the baseline sessions.

Known limitations

  • Single institution and mostly one scanner vendor, so external validity is limited.
  • Most segmentations are automatic and unreviewed; only 232 were manually corrected.
  • MGMT and IDH status are missing for many patients and were not re-validated beyond the medical records.
  • The NIfTI images are in atlas space and do not align with the DICOM images.

Cohort

Aggregate numbers from the sources below. Bars are relative to the 630 subjects.

Sex

  • Female 252 40%
  • Male 378 60%

Age

mean 62.7± 12.5 · range 18 to 89
0
100
200
300
367
18-2930-4950-6970+

Contrast combinations

How many subjects have exactly each set of contrasts.

T1wT1w_ceT2wFLAIRdwidscSubjects with exactly this set
491
70
63
6

Modality

subjects

  • MRI 630 100%
  • Pathology slides 34 5%

Contrast / sequence

subjects, values can overlap

  • T1-weighted 630 100%
  • T1-weighted, contrast enhanced 630 100%
  • T2-weighted 630 100%
  • FLAIR 630 100%
  • Diffusion-weighted 554 88%
  • DSC perfusion 497 79%

Condition

subjects, values can overlap

  • Glioblastoma 630 100%

Scanner vendor

subjects

  • Siemens Healthineers 622 99%
  • GE HealthCare 8 1%

Field strength

studies

  • 3 T 596 89%
  • 1.5 T 74 11%

License and access

Our reading of the license, not legal advice. Before you use the data, read the original license and confirm that your use is allowed. We take no responsibility for how you use a dataset. Full disclaimer

Access
Open download

Download without an account

DICOM via the TCIA Data Retriever; pre-processed NIfTI images, segmentations and histopathology slides via IBM Aspera; clinical, acquisition and radiomic tables as direct CSV downloads.

Access page

Creative Commons Attribution 4.0 International

Use, share and adapt the data for any purpose, including commercial use, as long as you credit the creators.

Every item on the TCIA collection page is listed under CC BY 4.0. TCIA also asks users to follow its Data Usage Policy and to cite the dataset DOI.

Original license text Version read: 4.0 Checked 2026-10-07

What you can do

  • Yes
  • Yes
  • Yes
  • Yes

What you can share

  • Yes
  • Yes
  • Yes

What you must do

  • Yes
  • Share alike No
  • No
  • No
  • Manuscript review No
  • Release code No
  • Return results No
  • Delete after use No

Limits

  • No
  • Location limits No

Citation

Bakas S, Sako C, Akbari H, et al. The University of Pennsylvania glioblastoma (UPenn-GBM) cohort: advanced MRI, clinical, genomics, & radiomics. Scientific Data 9, 453 (2022). https://doi.org/10.1038/s41597-022-01560-7. Data: Bakas S, et al. (2021). Multi-parametric magnetic resonance imaging (mpMRI) scans for de novo Glioblastoma (GBM) patients from the University of Pennsylvania Health System (UPENN-GBM) (Version 2) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.709X-DN49

All numbers

Every number on this page, as stored in stats.csv, with its source.

MeasureBreakdownValueSource
Subjectstotal 630bakas2022
Methods, Data
Subjectscondition=glioblastoma
de novo glioblastoma
630bakas2022
Abstract
Subjectsmodality=MR 630tcia-upenn-gbm
Data Access (Version 2)
Subjectsmodality=SM
subjects with histopathology slides
34tcia-upenn-gbm
Data Access (Version 2)
Studiestotal
611 pre-operative baseline and 60 follow-up scan sessions
671bakas2022
Table 1
Subjectssex=female 252bakas2022
Table 1
Subjectssex=male 378bakas2022
Table 1
Subjectsage=18-29 14bakas2022
Table 1
Subjectsage=30-49 69bakas2022
Table 1
Subjectsage=50-69 367bakas2022
Table 1
Subjectsage=70+ 180bakas2022
Table 1
Minimum agetotal
age range 18-89
18bakas2022
Methods, Clinical data
Maximum agetotal
age range 18-89
89bakas2022
Methods, Clinical data
Mean agetotal
age at the first available scan of each of the 630 subjects
62.7tcia-upenn-gbm-clinical
ID, Age_at_scan_years
Median agetotal
age at the first available scan of each of the 630 subjects
63.4tcia-upenn-gbm-clinical
ID, Age_at_scan_years
Age SDtotal
age at the first available scan of each of the 630 subjects
12.5tcia-upenn-gbm-clinical
ID, Age_at_scan_years
Studiescontrast=T1w
structural scans (T1; T1-Gd; T2; T2-FLAIR) in every session
671bakas2022
Table 1
Studiescontrast=T1w_ce 671bakas2022
Table 1
Studiescontrast=T2w 671bakas2022
Table 1
Studiescontrast=FLAIR 671bakas2022
Table 1
Studiescontrast=dwi
DTI
592bakas2022
Table 1
Studiescontrast=dsc 534bakas2022
Table 1
Studiescontrast_set=dsc+dwi+FLAIR+T1w+T1w_ce+T2w 527tcia-upenn-gbm-availability
Structural imaging, DTI imaging, DSC imaging
Studiescontrast_set=FLAIR+T1w+T1w_ce+T2w 72tcia-upenn-gbm-availability
Structural imaging, DTI imaging, DSC imaging
Studiescontrast_set=dwi+FLAIR+T1w+T1w_ce+T2w 65tcia-upenn-gbm-availability
Structural imaging, DTI imaging, DSC imaging
Studiescontrast_set=dsc+FLAIR+T1w+T1w_ce+T2w 7tcia-upenn-gbm-availability
Structural imaging, DTI imaging, DSC imaging
Subjectscontrast=T1w 630tcia-upenn-gbm-availability
ID, Structural imaging
Subjectscontrast=T1w_ce 630tcia-upenn-gbm-availability
ID, Structural imaging
Subjectscontrast=T2w 630tcia-upenn-gbm-availability
ID, Structural imaging
Subjectscontrast=FLAIR 630tcia-upenn-gbm-availability
ID, Structural imaging
Subjectscontrast=dwi
in at least one session
554tcia-upenn-gbm-availability
ID, DTI imaging
Subjectscontrast=dsc
in at least one session
497tcia-upenn-gbm-availability
ID, DSC imaging
Subjectscontrast_set=dsc+dwi+FLAIR+T1w+T1w_ce+T2w
contrasts pooled over a subject's sessions
491tcia-upenn-gbm-availability
ID, Structural imaging, DTI imaging, DSC imaging
Subjectscontrast_set=FLAIR+T1w+T1w_ce+T2w
contrasts pooled over a subject's sessions
70tcia-upenn-gbm-availability
ID, Structural imaging, DTI imaging, DSC imaging
Subjectscontrast_set=dwi+FLAIR+T1w+T1w_ce+T2w
contrasts pooled over a subject's sessions
63tcia-upenn-gbm-availability
ID, Structural imaging, DTI imaging, DSC imaging
Subjectscontrast_set=dsc+FLAIR+T1w+T1w_ce+T2w
contrasts pooled over a subject's sessions
6tcia-upenn-gbm-availability
ID, Structural imaging, DTI imaging, DSC imaging
Studiesvendor=siemens 663tcia-upenn-gbm-acquisition
Manufacturer
Studiesvendor=ge 8tcia-upenn-gbm-acquisition
Manufacturer
Subjectsvendor=siemens 622tcia-upenn-gbm-acquisition
ID, Manufacturer
Subjectsvendor=ge 8tcia-upenn-gbm-acquisition
ID, Manufacturer
Studiesfield_strength=3
one more session reports 2.89 T
596tcia-upenn-gbm-acquisition
Magnetic Field Strength
Studiesfield_strength=1.5 74tcia-upenn-gbm-acquisition
Magnetic Field Strength
Scanstotal
MR DICOM series
3,680tcia-upenn-gbm
Data Access (Version 2)
Imagestotal
MR DICOM image files
828,234tcia-upenn-gbm
Data Access (Version 2)
Slidestotal
H&E whole-slide images in NDPI format
71tcia-upenn-gbm
Data Access (Version 2)
Slidescontrast=he 71tcia-upenn-gbm
Description

Sources

The keys used in the table above.