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Spatial-Temporal Mitosis Detection in Phase-Contrast Microscopy via Likelihood Map Estimation by 3DCNN

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Prerequisites

Installation

Python setting

Conda user

conda env create -f=requirement.yml
conda activate pytorch

Docker user

docker build ./docker
sh run_docker.sh

Data Preparation

CVPR 2019 Contest on Mitosis Detection in Phase Contrast Microscopy Image Sequences

To use dataset, prease follow the guideline. Now the dataset line was expired. If you want to use the dataset, please ask the contest organizers directly. https://ieeexplore.ieee.org/abstract/document/9328484?casa_token=XLj19UfXiEwAAAAA:TdwkxaQwKywNwzsnDje3GgSL6960XqGUxNVLLXu2RBpWyb85DTy2f1TEqJJYYa4E9SmVjrfEzg

How to use

  1. Candidate path image extraction based on the brightness
matlab -nodesktop -nosplash -r "candidate_extractor(dataset_directory, './output/')"
  1. Generate ground truth from candidate
python generate_ground_truth.py
  1. Train V-Net
python train.py
  1. Prediction by V-Net
python predict.py

Citation

If you use this code for your research, please cite:

@article{nishimura2020spatial,
  title={Spatial-Temporal Mitosis Detection in Phase-Contrast Microscopy via Likelihood Map Estimation by 3DCNN},
  author={Nishimura, Kazuya and Bise, Ryoma},
  journal={arXiv preprint arXiv:2004.12531},
  year={2020}
}

mdmlm's People

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mdmlm's Issues

q

Hi! Do you process the downloaded dataset directly on MATLAB? Are there any other pre-treatments? I saw a file description in the URL where I downloaded the dataset, as if I was going to do R code processing. I would like to ask if you have to deal with it this way?
I also have a question, when I run the matlab code, the result of running it is Chinese empty, do you know why?
document.pdf

matlab code

Excuse me. The location of my image dataset is 'E:\C2C12\dataset_01',I want to create a new folder to store the results of code runs. So I write the input path as “indir_path='E:\C2C12\dataset_01'” and the output path as “outdir_path='E:\C2C12\processed_01'”.But the code runs incorrectly. Can you help me point out the error there? I put a screenshot of the code below. When looking for the image dataset, I did not contact the author, but I found a web link to the dataset. The link is https://osf.io/ysaq2/. I would like to ask if when you download the image dataset, do you put all the images in one folder or put the sixteen subfolders under one total folder. Thank you very much!
picture.pdf

matlab

I also have a problem, I changed indir to indir_path and outdir to outdir_path. The matlab code can run, but the resulting folder is empty. Do you know why this is?Below is a screenshot of my problem code.Thank you so much!
picture.pdf

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