cell_counting_v2

The repository includes the code for training cell counting applications. (Keras + Tensorflow)

Dataset can be downloaded here : http://www.robots.ox.ac.uk/~vgg/research/counting/index_org.html

Related Papers:

[1] Microscopy Cell Counting with Fully Convolutional Regression Networks.

http://www.robots.ox.ac.uk/~vgg/publications/2015/Xie15/weidi15.pdf

[2] U-Net: Convolutional Networks for Biomedical Image Segmentation.

https://arxiv.org/abs/1505.04597

To make the training easier, I added Batch Normalization to all architectures (FCRN-A and U-Net simple version).

Though still contains tiny difference with the original Matconvnet implementation, for instance, upsampling in Keras is implemented by repeating elements, instead of bilinear upsampling. So, to mimic the bilinear upsampling, I did upsampling + convolution. Also, more data augmentation needs to be added. Nevertheless. I'm able to get similar results as reported in the paper.

In all architectures, they follow the fully convolutional idea, each architecture consists of a down-sampling path, followed by an up-sampling path. During the first several layers, the structure resembles the cannonical classification CNN, as convolution, ReLU, and max pooling are repeatedly applied to the input image and feature maps. In the second half of the architecture, spatial resolution is recovered by performing up-sampling, convolution, eventually mapping the intermediate feature representation back to the original resolution.

In the U-net version, low-level feature representations are fused during upsampling, aiming to compensate the information loss due to max pooling. Here, I only gave a very simple example here (64 kernels for all layers), not tuned for any dataset.

As people know, Deep Learning is developing extremely fast today, both papers were published two years ago, which is quite "old". If people are interested in cell counting, feel free to edit on this.