SoloIMC

An IMC Necleus Instance Segmentation Tool using SOLOv2.

Quick Start

Requirements

Linux (Windows is not officially supported)
Python 3.5+
PyTorch 1.1 or higher (>=1.5 is not tested)
CUDA 9.0 or higher
NCCL 2
GCC 4.9 or higher
mmcv 0.2.16

or use the provided yaml file solov2-pytorch1.4-environment.yaml (with Python = 3.7, PyTorch = 1.4, CUDA = 10.1, GCC = 5.5).

Download SoloIMC

git-lfs clone https://github.com/Liuzhe30/SoloIMC

Install SOLO

SOLOv2 implementation is based on mmdetection(v1.0.0). Please refer to the official document for installation.

a. Create a conda virtual environment and activate it.

conda create -n solo python=3.7 -y
conda activate solo

b. Install PyTorch and torchvision following the official instructions, e.g.,

conda install pytorch torchvision -c pytorch

c. Clone the SOLO repository.

git clone https://github.com/WXinlong/SOLO.git
cd SOLO

d. Install build requirements and then install SOLO. (We install pycocotools via the github repo instead of pypi because the pypi version is old and not compatible with the latest numpy.)

pip install -r requirements/build.txt
pip install "git+https://github.com/cocodataset/cocoapi.git#subdirectory=PythonAPI"
pip install -v -e .  # or "python setup.py develop"

Dataset Preparation

python3 mask_recreator.py

If you want to recreate the annotation files, please run the following commands:

pip install cython
pip install git+git://github.com/waspinator/coco.git@2.1.0
python3 mask_annotation.py
python3 mask_pycococreator.py

Usage

Train with single GPU

cd SOLO
python tools/train.py ${CONFIG_FILE}

Example:
python tools/train.py configs/solov2_r50_fpn_8gpu_1x_imc.py

Testing

# single-gpu testing
python tools/test_ins.py ${CONFIG_FILE} ${CHECKPOINT_FILE} --show --out  ${OUTPUT_FILE} --eval segm

Example: 
python tools/test_ins.py configs/solov2_r50_fpn_8gpu_1x_imc.py  work_dirs/solov2_release_r50_fpn_8gpu_1x/epoch_10.pth --show --out  results_solo.pkl --eval segm

Visualization

python tools/test_ins_vis.py ${CONFIG_FILE} ${CHECKPOINT_FILE} --show --save_dir  ${SAVE_DIR}

Example: 
python tools/test_ins_vis.py configs/solov2_r50_fpn_8gpu_1x_imc.py  work_dirs/solov2_release_r50_fpn_8gpu_1x/epoch_10.pth --show --save_dir  work_dirs/vis_solo

Contributing to the project

Any pull requests or issues are welcome.

Progress

README for running SoloIMC.