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基于飞桨的无标记细胞图像虚拟染色


本项目是基于飞桨框架的细胞虚拟染色技术实现,采用的模型是基于自注意力机制的3D Res-UNet。 项目实现参考了:https://github.com/AllenCellModeling/pytorch_fnet/tree/release_1 以及飞桨官方平台:https://www.paddlepaddle.org.cn/


数据集

数据集下载地址:http://downloads.allencell.org/publication-data/label-free-prediction/index.html
数据集名称与图像数据对应关系:
nucleoli ---- fibrillarin
nuclear envelope ---- lamin_b1
microtubule images ---- alpha_tubulin
actin filament ---- beta_actin
mitochondria ---- tom20
cell membrane ---- membrane_caax_63x
endoplasmic reticulum ---- sec61_beta
dna ---- myosin_iib
(DIC) nuclear envelope ---- dic_lamin_b1
actomyosin bundles ---- myosin_iib
tight junctions ---- zo1
golgi ---- st6gal1
desmosome ---- desmoplakin\


模型训练

终端远程代码示例:

./scripts/train.sh  [dataset] [gpu_id] [model_name]

以fibrillarin为例,首先cd到项目文件夹下,终端运行./scripts/train.sh fibrillarin -1 gvtnet

其中fibrillarin表示我们要训练细胞核仁预测模型,-1表示使用CPU进行训练,gvtnet表示我们将我们的模型命名为gvtnet。其中dic_lamin_b1andmembrane_caax_63x例外,其训练命令如下:

./scripts/train_dic.sh [gpu_id] [model_name]
./scripts/train_membrane.sh [gpu_id] [model_name]

模型预测

终端远程代码示例:

./scripts/predict.sh  [dataset] [gpu_id] [model_name] [checkpoint_num]

以fibrillarin为例,首先cd到项目文件夹下,终端运行./scripts/predict.sh fibrillarin -1 gvtnet 10000,其中dic_lamin_b1andmembrane_caax_63x例外,其预测命令如下:

./scripts/predict_dic.sh [gpu_id] [model_name] [checkpoint_num]
./scripts/predict_membrane.sh [gpu_id] [model_name] [checkpoint_num]

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