Segmentation of neurons in microscopy images

版本 1.0.3 (1.3 MB) 作者: Omer Yuval

Set up, train and apply a neural network for segmentation of neurons in microscopy images.

https://github.com/Omer1Yuval1/Neuronalyzer

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更新时间 2021/8/13

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Quick start:

0. Set network and training parameters in Params.m.

1. Prepare input and output images:

Im_In = {Im_In_1,Im_In_2,Im_In_3};

Im_Out = {Im_Out_1,Im_Out_2,Im_Out_3};

2. Generate training set:

Generate_Dataset(Im_In,Im_Out);

3. Train:

net = Train;

4. Apply the trained network to an image:

[Im_Out,Im_Label] = Segment_Neuron(net,Im_In_4);

imshow(Im_Label);

* Example raw and annotated neuron images can be found in this paper [1].

* An example pre-trained network is included.

* Please cite this paper [1].

Advanced options:

- Control sample size (see "Input_Size" in Params.m).

- Control class weights during training (see "Class_Weights" in Params.m).

- Control the minimum number of neuron pixels in training samples (see "Functions" block in Params.m).

- You can generate the training set locally and train on another machine (see "Paths" block in Params.m).

1. Yuval, O., Iosilevskii, Y., Meledin, A., Podbilewicz, B., & Shemesh, T. (2021). Neuron tracing and quantitative analyses of dendritic architecture reveal symmetrical three-way-junctions and phenotypes of git-1 in C. elegans. PLoS computational biology, 17(7), e1009185.

引用格式

Omer Yuval (2024). Segmentation of neurons in microscopy images (https://www.mathworks.com/matlabcentral/fileexchange/97547-segmentation-of-neurons-in-microscopy-images), MATLAB Central File Exchange. 检索时间: 2024/11/22.

Yuval, Omer, et al. “Neuron Tracing and Quantitative Analyses of Dendritic Architecture Reveal Symmetrical Three-Way-Junctions and Phenotypes of Git-1 in C. Elegans.” PLOS Computational Biology, edited by Hugues Berry, vol. 17, no. 7, Public Library of Science (PLoS), July 2021, p. e1009185, doi:10.1371/journal.pcbi.1009185.

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Sciences > Neuroscience > Cellular Neuroscience > Microscopy >

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版本	已发布	发行说明
1.0.3	2021/8/13	Changed the image.	下载
1.0.2	2021/8/13	Edited the description.	下载
1.0.1	2021/8/13	Edited the description.	下载
1.0.0	2021/8/13		下载

MLA	Yuval, Omer, et al. “Neuron Tracing and Quantitative Analyses of Dendritic Architecture Reveal Symmetrical Three-Way-Junctions and Phenotypes of Git-1 in C. Elegans.” PLOS Computational Biology, edited by Hugues Berry, vol. 17, no. 7, Public Library of Science (PLoS), July 2021, p. e1009185, doi:10.1371/journal.pcbi.1009185.
APA	Yuval, O., Iosilevskii, Y., Meledin, A., Podbilewicz, B., & Shemesh, T. (2021). Neuron tracing and quantitative analyses of dendritic architecture reveal symmetrical three-way-junctions and phenotypes of git-1 in C. elegans. (H. Berry, Ed.)PLOS Computational Biology, 17(7), e1009185. Public Library of Science (PLoS). Retrieved from https://doi.org/10.1371%2Fjournal.pcbi.1009185
BibTeX	@article{Yuval_2021, doi = {10.1371/journal.pcbi.1009185}, url = {https://doi.org/10.1371%2Fjournal.pcbi.1009185}, year = 2021, month = {jul}, publisher = {Public Library of Science ({PLoS})}, volume = {17}, number = {7}, pages = {e1009185}, author = {Omer Yuval and Yael Iosilevskii and Anna Meledin and Benjamin Podbilewicz and Tom Shemesh}, editor = {Hugues Berry}, title = {Neuron tracing and quantitative analyses of dendritic architecture reveal symmetrical three-way-junctions and phenotypes of git-1 in C. elegans}, journal = {{PLOS} Computational Biology} }