Prompt-Guided Interactive Segmentation of Interstitial Lung Disease in Thoracic CT
Authors: Vasilis Dedousis, Lubnaa Abdur Rahman, Lorenzo Brigatο, Ethan Dack, Andreas Christe, Christoph Frank, Manuela Funke-Chambour, Justus Roos, Adrian Huber, Lukas Ebner, Stavroula Mougiakakou
Organizations: University of Bern, Bern, Switzerland · Graduate School for Cellular and Biomedical Sciences, Bern, Switzerland · Department of Diagnostic, Interventional, and Pediatric Radiology, Bern University Hospital, Bern, Switzerland · Department of Radiology, Lucern Cantonal Hospital, Lucern, Switzerland · Division of Pulmonology, Department of Medicine, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
Accurate segmentation of interstitial lung disease (ILD) patterns is essential for quantitative disease assessment and longitudinal monitoring. However, existing approaches remain limited by relying on dense annotations and producing static predictions that cannot be refined, motivating interactive approaches. While promptable models show promise in interactive segmentation, their adaptation to ILDs remains largely unexplored. To address this gap, we investigate prompt-guided foundation models for ILD refinement and present, to the best of our knowledge, the first adaptation of MedSAM2 for interactive 3D ILD segmentation on thoracic CT. We investigate three fine-tuning strategies and multiple clinically motivated prompts: bounding-boxes (BBox), point, lasso, and scribble. On a dataset spanning seven ILD patterns and healthy lung tissue, full model fine-tuning performed best, improving the average Dice score by 4.7 percentage points over MedSAM2.While BBox prompts achieve the strongest performance, non-native MedSAM2 interactions such as lasso and scribble prompts also prove effective. Finally, we present and evaluate a proof-of-concept end-to-end workflow in which MedSAM2 is initialized from an automatic segmentation prior and subsequently refined using radiologist prompts. Model weights and plug-ins made available at: https://github.com/AIHNlab/ILD-SemiSegTool.
Figures & tables
Split
Healthy
GGO
Ret.
Cons.
HC
Ret.+GGO
Bron.
Emph.
Train
243
148
150
6
210
28
7
118
Val
31
19
21
1
28
4
2
14
Test
32
19
24
1
26
4
1
18
Total
306
186
195
8
264
36
10
150
Table 1: Case distribution of ILD patterns across dataset.
Figure 1: Interactive segmentation framework. (a) Radiologist prompts drive FT MedSAM2 to segment CT images, optionally initialized from an automatic segmentation (PoC); prompts are simulated from ground-truth masks. (b) Prompts on a bronchiectasis slice, including single-BBox, multi-BBox, points, lasso, scribble, with GT on top row and FT MedSAM2 output on bottom row.
Learning rate
Weight decay
Loss weights
5e-5 , 1.7e-5 , 1.7e-4, 5e-4
1e-4 , 1e-1
{0.1,1,10} orthogonal; (1,1,1) , (10,10,10)
Table 2: Grid search for MedSAM2 fine-tuning. Bold , underline , and italic denote the optimal configuration for full finetuning, mask only, and mask and memory, respectively.
SBBox
MBBox
Points
Lasso
Scribble
Model
DSC
NSD
DSC
NSD
DSC
NSD
DSC
NSD
DSC
NSD
SAM 2.1
0.255
0.206
0.340
0.319
0.183
0.094
0.213
0.133
0.280
0.226
MedSAM2
0.347
0.323
0.337
0.314
0.333
0.298
0.359
0.322
0.318
0.280
nnInteractive
0.333
0.273
0.398
0.313
0.195
0.181
0.041
0.074
0.376
0.325
MO (Ours)
0.383 ⋆ ⋆
0.349 ⋆
0.418 ⋆ ⋆
0.365 ⋆ ⋆
0.355 ⋆ ⋆
0.316 ⋆
0.399 ⋆ ⋆
0.348 ⋆ ⋆
0.383 ⋆
0.333
MM (Ours)
0.373 ⋆
0.327 ⋆
0.418 ⋆ ⋆
0.374 ⋆ ⋆
0.349 ⋆
0.301 ⋆
0.400 ⋆ ⋆
0.344 ⋆
0.396 ⋆
0.346 ⋆ ⋆
Table 3: Performance across prompt types (3D, mid-slice init ) comparing baselines and standalone fine-tuning strategies: MO, MM, and FF. Best in bold , second best underlined . ⋆ / ▽ : significantly better/worse than MedSAM2; ⋆ / ▽ : significantly better/worse than nnInteractive (paired Wilcoxon signed-rank test, case-averaged, Holm–Bonferroni corrected, p<0.05 ). Unmarked cells: no statistical significance.
Figure 2: Evaluation of FF MedSAM2. (a) Per-pattern DSC across prompt types in 2D and 3D. (b) Sensitivity of 3D performance to initialization slice: average DSC and NSD versus offset from the middle ground-truth slice (0%); dashed lines indicate initialization from the ground-truth slice with the most foreground.
Model
Prompt
Bron.
Cons.
Emph.
GGO
HC
Ret.
Ret.+GGO
Healthy
Case Avg.
MedSAM2
SBBox
0.128
0.610
0.177
0.131
0.068
0.149
0.352
0.832
0.347
MBBox
0.128
0.610
0.157
0.140
0.075
0.174
0.365
0.777
0.337
Points
0.139
0.043
0.148
0.155
0.059
0.143
0.232
0.831
0.333
Lasso
0.139
0.043
0.184
0.192
0.099
0.202
0.236
0.809
0.359
Scribble
0.133
0.043
0.173
0.155
0.087
0.158
0.221
0.733
0.318
nnInteractive
SBBox
0.480
0.553
0.249
0.115
0.064
0.112
0.218
0.790
0.333
Table 4: Per-pattern DSC of baseline models nnInteractive and MedSAM2.
Model
Prompt
Bron.
Cons.
Emph.
GGO
HC
Ret.
Ret.+GGO
Healthy
Case Avg.
nnU-Net
–
0.039
0.006
0.346
0.526
0.464
0.397
0.276
0.922
0.504
nnInteractive + MP
SBBox
0.073
0.006
0.283
0.165
0.093
0.124
0.134
0.869
0.291
MBBox
0.085
0.006
0.346
0.178
0.166
0.197
0.240
0.700
0.304
Points
0.074
0.006
0.297
0.191
0.113
0.167
0.200
0.805
0.300
Lasso
0.055
0.006
0.306
0.204
0.165
0.191
0.239
0.802
0.323
Scribble
0.084
0.006
0.323
0.155
0.125
0.152
0.246
0.788
0.299
Table 5: Per-pattern DSC across prompt types for PoC pipeline. Best per column in bold , second best underlined . Significance reported on Case Avg. only (paired Wilcoxon, 32 volumes, Holm–Bonferroni corrected): ⋆ / ▽ significantly better/worse than nnU-Net; ⋆ / ▽ significantly better/worse than nnInteractive+MP. Unmarked: no statistical significance. Case Avg. averaged across prompts: 0.448 (FF+MP P+N), 0.434 (FF+MP P), 0.501 (FF+MP N), 0.303 (nnInteractive+MP).
Medical image segmentation delineates organs, lesions, and other structures in scans to support measurement, diagnosis, treatment planning, and research.
Department of Biomedical Engineering, Johns Hopkins University · Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University · Department of Computer Science, Johns Hopkins University +1