LSnyd/Cell-DETR

Official and maintained implementation of the paper Attention-Based Transformers for Instance Segmentation of Cells in Microstructures [BIBM 2020].

Cell-DETR: Attention-Based Transformers for Instance Segmentation of Cells in Microstructures

Tim Prangemeier, Christoph Reich & Heinz Koeppl

This repository includes the official and maintained implementation of the paper Attention-Based Transformers for Instance Segmentation of Cells in Microstructures (BIBM 2020).

Abstract

Detecting and segmenting object instances is a common task in biomedical applications. Examples range from detecting lesions on functional magnetic resonance images, to the detection of tumours in histopathological images and extracting quantitative single-cell information from microscopy imagery, where cell segmentation is a major bottleneck. Attention-based transformers are state-of-the-art in a range of deep learning fields. They have recently been proposed for segmentation tasks where they are beginning to outperforming other methods. We present a novel attention-based cell detection transformer (Cell-DETR) for direct end-to-end instance segmentation. While the segmentation performance is on par with a state-of-the-art instance segmentation method, Cell-DETR is simpler and faster. We showcase the method's contribution in a the typical use case of segmenting yeast in microstructured environments, commonly employed in systems or synthetic biology. For the specific use case, the proposed method surpasses the state-of-the-art tools for semantic segmentation and additionally predicts the individual object instances. The fast and accurate instance segmentation performance increases the experimental information yield for a posteriori data processing and makes online monitoring of experiments and closed-loop optimal experimental design feasible.

Architecture

Architecture of the end-to-end instance segmentation network, with brightfield specimen image input and an instance segmentation prediction as output. The backbone CNN encoder extracts image features that then feed into both the transformer encoder-decoder for class and bounding box prediction, as well as to the CNN decoder for segmentation. The transformer encoded features, as well as the transformer decoded features, are feed into a multi-head-attention module and together with the image features from the CNN backbone feed into the CNN decoder for segmentation. Skip connections additionally bridge between the backbone CNN encoder and the CNN decoder. Input and output resolution is 128 × 128 pixels.

Dependencies

The Cell-DETR implementation uses multiple existing implementations. First, deformable convolutions v2 [2] are used based on the implementation of Dazhi Cheng. Second, pade activation units [4] are utilized base on the official implementation, by the authors. And third, the pixel adaptive convolutions [3] implementation by Nvidia is used. The pade activation unit implementation as well as the pixel adaptive convolution implementation are adopted slightly and are included in this repository. All dependencies can be installed by exicuting the following commands

git submodule add https://github.com/LSnyd/Cell-DETR.git
cd Cell-DETR
pip install -r requirements.txt
git submodule add https://github.com/chengdazhi/Deformable-Convolution-V2-PyTorch
cd Deformable-Convolution-V2-PyTorch
git checkout pytorch_1.0.0
python setup.py build install
cd ../pade_activation_unit/cuda

Before building and installing the pade_activation_unit, it may be necessary to cancel out the extra_compile_args in the setup.py (line 312-314) file in the cuda folder:

# extra_compile_args={'cxx': [],
# 'nvcc': ['-gencode=arch=compute_60,code="sm_60,compute_60"', '-lineinfo',
#  "-ccbin=gcc-6.3.0"]}

Afterwards run:

python setup.py build install

The transformer [5] implementation is based on the official implementation of DETR [1].

Usage

CELL-DETR can be trained, validated and testes by using the main.py script. The following command line arguments define what actions are performed.

python main.py {+ args}

Argument	Default value	Info
--train	False	Binary flag. If set training will be performed.
--val	False	Binary flag. If set validation will be performed.
--test	False	Binary flag. If set testing will be performed.
--cuda_devices	"0"	String of cuda device indexes to be used. Indexes must be separated by a comma
--data_parallel	False	Binary flag. If multi GPU training should be utilized set flag.
--cpu	False	Binary flag. If set all operations are performed on the CPU.
--epochs	200	Number of epochs to perform while training.
--lr_schedule	False	Binary flag. If set the learning rate will be reduced after epoch 50 and 100.
--ohem	False	Binary flag. If set online heard example mining is utilized.
--ohem_fraction	0.75	Ohem fraction to be applied when performing ohem.
--batch_size	4	Batch size to be utilized while training.
--path_to_data	"trapped_yeast_cell_dataset"	Path to dataset.
--augmentation_p	0.6	Probability that data augmentation is applied on training data sample.
--lr_main	1e-04	Learning rate of the detr model (excluding backbone).
--lr_backbone	1e-05	Learning rate of the backbone network.
--no_pac	False	Binary flag. If set no pixel adaptive convolutions will be utilized in the segmentation head.
--load_model	""	Path to model to be loaded.
--dropout	0.0	Dropout factor to be used in model.
--three_classes	False	Binary flag, If set three classes (trap, cell of interest and add. cells) will be utilized.
--softmax	False	Binary flag, If set a softmax will be applied to the segmentation prediction instead sigmoid.
--only_train_segmentation_head_after_epoch	200	Number of epoch where only the segmentation head is trained.
--lr_segmentation_head	1e-05	Learning rate of the segmentation head, only applied when seg head is trained exclusively.
--no_deform_conv	False	Binary flag. If set no deformable convolutions will be utilized.
--no_pau	False	Binary flag. If set no pade activation unit is utilized, however, a leaky ReLU is utilized.

For training, validating and testing of the Cell-DETR B architecture run

python main.py --train --val --test --path_to_data "trapped_yeast_cell_dataset" --lr_schedule --batch_size 10 --data_parallel --cuda_devices "0, 1" --softmax

For training, validating and testing of the Cell-DETR A architecture run

python main.py --train --val --test --path_to_data "trapped_yeast_cell_dataset" --lr_schedule --batch_size 10 --data_parallel --cuda_devices "0, 1" --softmax --no_pac --no_deform_conv --no_pau

Trained Models

Our trained models (Cell-DETR A & B) are included in the folder trained_models.

To load and test the trained Cell-DETR A model run

python main.py --test --path_to_data "trapped_yeast_cell_dataset" --cuda_devices "0" --softmax --no_pac --no_deform_conv --no_pau --load_model "trained_models/Cell_DETR_A"

to load and test the trained Cell-DETR B model run

python main.py --test --path_to_data "trapped_yeast_cell_dataset" --cuda_devices "0" --softmax --load_model "trained_models/Cell_DETR_B"

Data

A few toy/test examples of the trapped yeast cell instance segmentation dataset are included in folder trapped_yeast_cell_dataset. The full dataset can be requested from the author's.

Results

Qualitative results

Example segmentations of our Cell-DETR B model.

Segmentation results

Model	Dice	Accuracy	mIoU (mean over instances)	Cell IoU
Cell-DETR A	0.92	0.96	0.84	0.83
Cell-DETR B	0.92	0.96	0.85	0.84

Bounding box results

Model	MSE	L1	IoU	gIoU
Cell-DETR A	0.0006	0.016	0.81	0.80
Cell-DETR B	0.0005	0.016	0.81	0.81

Classification results

Model	Accuracy
Cell-DETR A	1.0
Cell-DETR B	1.0

Citation

If you find this research useful in your work, please acknowledge it appropriately and cite the paper:

@article{prangemeier2020c,
        title={Attention-Based Transformers for Instance Segmentation of Cells in Microstructures},
        author={Prangemeier, Tim and Reich, Christoph and Koeppl, Heinz},
        booktitle={2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
        year={2020}
}

References

[1] @article{carion2020end,
        title={End-to-End Object Detection with Transformers},
        author={Carion, Nicolas and Massa, Francisco and Synnaeve, Gabriel and Usunier, Nicolas and Kirillov, Alexander and Zagoruyko, Sergey},
        journal={arXiv preprint arXiv:2005.12872},
        year={2020}
}

[2] @inproceedings{zhu2019deformable,
        title={Deformable convnets v2: More deformable, better results},
        author={Zhu, Xizhou and Hu, Han and Lin, Stephen and Dai, Jifeng},
        booktitle={Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition},
        pages={9308--9316},
        year={2019}
}

[3] @inproceedings{su2019pixel,
        title={Pixel-adaptive convolutional neural networks},
        author={Su, Hang and Jampani, Varun and Sun, Deqing and Gallo, Orazio and Learned-Miller, Erik and Kautz, Jan},
        booktitle={Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition},
        pages={11166--11175},
        year={2019}
}

[4] @article{molina2019pad,
        title={Pad$\backslash$'e Activation Units: End-to-end Learning of Flexible Activation Functions in Deep Networks},
        author={Molina, Alejandro and Schramowski, Patrick and Kersting, Kristian},
        journal={arXiv preprint arXiv:1907.06732},
        year={2019}
}

[5] @inproceedings{vaswani2017attention,
        title={Attention is all you need},
        author={Vaswani, Ashish and Shazeer, Noam and Parmar, Niki and Uszkoreit, Jakob and Jones, Llion and Gomez, Aidan N and Kaiser, {\L}ukasz and Polosukhin, Illia},
        booktitle={Advances in neural information processing systems},
        pages={5998--6008},
        year={2017}
}