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Lymph nodes on CT, the marked nodes only, segmentation

CT Lymph Nodes, mediastinum

A contrast-enhanced CT of the chest, abdomen and pelvis of an NIH Clinical Center patient, the marked enlarged lymph nodes of the mediastinum traced by hand (CT Lymph Nodes, the 90 MED_LYMPH patients).

10 test caseslungimage CT
Look at the images
Read before comparing (8)
  • Truth. Radiologists marked the nodes; masks traced by hand, apart from the marks, followed in December 2015. The collection page says neither who traced them nor with which tool, and the paper it cites, Seff et al., MICCAI 2015, could not be read. Graded expert on the page's word; one tracing, no agreement between readers reported.
  • Label. Only the marked nodes are traced, 1 to 31 a scan on the ten test CTs (3 at the median). The marks measure 11.9 to 17.5 mm in short axis between quartiles (median 14.3 mm, one of 388 under 10 mm): enlarged nodes by RECIST. Nothing says every enlarged node was marked, and nodes of normal size were not.
  • Scoring. A node the method finds and the tracers left counts as an error, right or not: the scores measure agreement with the marked set, not node detection. On the 25 twin scans, a perfect map of both copies' nodes scores a median Dice of 0.49 (0.03 to 0.98) against the mediastinal mask. structures.json reads 'lymph node' as mediastinal_lymph_node, so a general node segmenter should name other nodes apart.
  • Twins. The 25 scans held twice carry the mediastinal nodes on one copy and the abdominal nodes on the other, which the collection page does not say; their masks share size, voxel size and origin, and the pair read whole holds the same voxels. MED_LYMPH_002 and 040 (test) and 038, 060 and 074 (development) are such scans. With no patient identifier, a patient scanned on other days could not be told.
  • Images. The headers hold only sex and age: no scanner, kernel, contrast agent or true date. The scans run from the neck or shoulders to the pelvis or thighs, portal-venous by their look, with oral contrast on most, in Hounsfield units: 0.68 to 0.98 mm in plane, slices 1 mm apart (1.5 mm on MED_LYMPH_075, 1.25 mm on five development CTs).
  • Nodes. The test nodes hold 1.8 to 130.3 ml in 1 to 13 pieces, touching nodes merging: MED_LYMPH_071 has 31 traced nodes in 13 pieces and 130 ml. The tracing is coarse in places, taking in some lung (142 of the 9,004 voxels of MED_LYMPH_002 under -500 HU) or vessel and bone (355 of the 3,236 of MED_LYMPH_075 over 300 HU).
  • Outside numbers. None: no segmentation challenge ran on these masks and the collection's papers report detection. TotalSegmentator has no lymph node class, so the labels were checked by eye only. Surface tolerance: 1 mm, the provider setting none. The masks are public since December 2015 and widely used for training: a model may have seen these test cases.
  • Overlap. No descriptor names the collection. The corpus's other NIH Clinical Center CTs, Pancreas-CT's in PancreasCT8 and PancreasCT8_Seg, cannot be matched by name; none of the 40 scans built for the two lymph node sets shares a slice with PancreasCT8's 20 fixed images of the same pixel size, and its resampled moving images could not be compared. MediastinalLymphNodesCT is another cohort, from Boston hospitals.

No method has a result on every case of this dataset yet.

Case by case

Click a score to look at that result: the image, the truth in green and the method's map in red. Underlined scores have their image; for the others you see the case without the result.

About the data

The first test case of CT Lymph Nodes, mediastinum
The first test caseClick to look at every case.
Test cases
10 test CTs drawn with seed 2026 among the 80 MED_LYMPH patients outside development, and 10 development CTs, the last of the same seeded order. 25 of the 90 scans are also in the collection under an ABD_LYMPH name (TWINS in prepare.py): they are cases here only, and CTLymphNodes_Abdomen leaves them out.
Truth
contours by experts the lymph nodes of the mediastinum that were marked on the scan, enlarged ones, traced by hand at the NIH Clinical Center, all in one label; the unmarked nodes of the mediastinum and every node elsewhere in the scan are background
Licence
CC BY 3.0
10 cases for tuning, never tested

MED_LYMPH_055, MED_LYMPH_060, MED_LYMPH_038, MED_LYMPH_062, MED_LYMPH_028, MED_LYMPH_023, MED_LYMPH_053, MED_LYMPH_048, MED_LYMPH_074, MED_LYMPH_039