mist-medical 2.0.1rc0

MIST is a simple and scalable end-to-end framework for medical imaging segmentation.

Medical Imaging Segmentation Toolkit

MIST is a simple, scalable, end-to-end framework for 3D medical image segmentation. It handles everything from raw NIfTI files to trained models and evaluated predictions, with sensible defaults that work well out of the box and a configuration file for when you need more control.

Installation

Training (NVIDIA GPU required):

pip install "mist-medical[train]"

Inference only (CPU-compatible):

pip install mist-medical

Development:

git clone https://github.com/mist-medical/MIST.git
cd MIST
pip install -e ".[train]"    # full
pip install -e .             # inference only

Quick Start

1. Prepare a dataset JSON describing your data:

{
    "task":        "brats2023",
    "modality":    "mr",
    "train-data":  "/full/path/to/raw/data/train",
    "test-data":   "/full/path/to/raw/data/validation",
    "mask":        ["seg.nii.gz"],
    "images":      {"t1": ["t1n.nii.gz"],
                    "t2": ["t2w.nii.gz"],
                    "tc": ["t1c.nii.gz"],
                    "fl": ["t2f.nii.gz"]},
    "labels":      [0, 1, 2, 3],
    "final_classes": {"WT": [1, 2, 3],
                      "TC": [1, 3],
                      "ET": [3]}
}

2. Run the full pipeline (analyze → preprocess → train → evaluate):

mist_run_all --data dataset.json \
             --numpy /path/to/numpy \
             --results /path/to/results

3. Run inference on new data:

mist_predict --models-dir /path/to/results/models \
             --config /path/to/results/config.json \
             --paths-csv /path/to/test.csv \
             --output /path/to/predictions

Key Features

• Automatic configuration — analysis step determines target spacing, patch size, normalization, and foreground cropping from your data
• Five-fold cross-validation by default, with custom fold assignment support
• Multi-GPU training via PyTorch DDP; uses all visible GPUs automatically
• GPU-accelerated data loading via NVIDIA DALI during training
• Sliding window inference with configurable overlap and patch blending
• Test-time augmentation and multi-model ensembling at inference
• Postprocessing with learnable, per-class morphological strategies
• CPU inference — mist_predict runs on any machine, including Macs

Supported Architectures

Model	Key
nnU-Net	nnunet
nnU-Net Pocket	nnunet-pocket
MedNeXt (small / base / medium / large)	mednext-small, mednext-base, mednext-medium, mednext-large
FMG-Net	fmgnet
W-Net	wnet
Swin UNETR (small / base / large)	swinunetr-small, swinunetr-base, swinunetr-large

Change the architecture in config.json or pass --model <key> at the command line.

Supported Loss Functions

Loss	Key	Notes
Dice	dice
Dice + Cross-Entropy	dice_ce
clDice	cldice	Composite
Boundary Loss	bl	Composite
Generalized Surface Loss	gsl	Composite
Hausdorff Distance One-Sided	hdos	Composite
Volumetric SDDL	volumetric_sddl	Composite
Vessel SDDL	vessel_sddl	Composite

Composite losses blend a region-based term with a boundary/distance term, weighted by a scheduled alpha. Schedules: constant, linear, cosine.

Pipeline Commands

Command	Description
mist_run_all	Run the full pipeline end-to-end
mist_analyze	Analyze dataset and generate config.json
mist_preprocess	Preprocess images into NumPy arrays
mist_train	Train models
mist_predict	Run inference on new data
mist_ensemble	Combine predictions from multiple models via STAPLE or majority vote
mist_evaluate	Evaluate predictions against ground truth
mist_postprocess	Apply postprocessing strategies
mist_rank	Rank multiple evaluation result CSVs BraTS-style
mist_average_weights	Average model weights across folds
mist_convert_msd	Convert Medical Segmentation Decathlon datasets
mist_convert_csv	Convert CSV-formatted datasets

Documentation

Full documentation, including configuration reference and advanced topics, is at mist-medical.readthedocs.io.

What's New

• June 2026 — 2.0.1 release candidate — BF16 automatic mixed precision replaces FP16 throughout training and inference, reducing memory use and eliminating gradient loss scaling. Sliding-window inference gains a tunable sw_batch_size parameter. mist_rank adds pairwise Wilcoxon significance testing via --significance-csv. Several targeted memory-reduction fixes land across the inference stack.
• June 2026 — Multi-model ensembling — mist_ensemble combines discrete NIfTI predictions from two or more separately trained models into a single consensus segmentation via STAPLE (--ensemble-backend staple, default) or majority vote (--ensemble-backend majority_vote). Works for single-class and multi-class label maps.
• May 2026 — 2.0.0 release candidate — BraTS-style multi-strategy ranking (mist_rank), a structured postprocessing transform registry with LLM-readable metadata (describe_transforms), and full pathlib + PEP 585/604 modernization across the codebase.
• April 2026 — CPU inference support — mist_predict now runs on any machine, including Macs and laptops without an NVIDIA GPU. Install with pip install mist-medical (no GPU required).
• March 2026 — Resume training — interrupted runs can be continued from the last checkpoint with --resume, with atomic checkpointing to prevent corruption.
• March 2026 — GPU-aware automatic patch size — the analysis step now derives the patch size from available GPU memory, so the default configuration is hardware-appropriate without manual tuning.
• March 2026 — Transfer learning — initialize encoders from pretrained weights with --pretrained-weights, and average model weights across folds with mist_average_weights.
• March 2026 — Better training defaults — AdamW optimizer and gradient clipping are now the defaults, with the clipping threshold exposed via grad_clip_norm in config.json.
• September 2025 — BraTS 2025 adult glioma challenge @ MICCAI 2025 — MIST takes 3rd place (repeat).
• November 2024 — MedNeXt models — small, base, medium, and large variants added (mednext-small, mednext-base, mednext-medium, mednext-large).
• October 2024 — BraTS 2024 adult glioma challenge @ MICCAI 2024 — MIST takes 3rd place.

Citation

If you use MIST in your work, please cite:

@article{celaya2024mist,
  title   = {MIST: A Simple and Scalable End-To-End 3D Medical Imaging Segmentation Framework},
  author  = {Celaya, Adrian and others},
  journal = {arXiv preprint arXiv:2407.21343},
  year    = {2024}
}

@article{celaya2022pocketnet,
  title   = {PocketNet: A Smaller Neural Network For Medical Image Analysis},
  author  = {Celaya, Adrian and others},
  journal = {IEEE Transactions on Medical Imaging},
  doi     = {10.1109/TMI.2022.3224873},
  year    = {2022}
}