From 839193fba0f23adeb4b1d4b7fdb1fbe4ecf83f9c Mon Sep 17 00:00:00 2001 From: Tanqiu Liu Date: Mon, 18 Sep 2017 22:18:12 -0500 Subject: [PATCH] Update README.md --- README.md | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 8f17f7f..87c0e5d 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ A sample image： ## Methods The detection process consists of 2 steps: 1) locating cell centers with a convolutional neural network(CNN), 2) detecting cell contour. -###1. Locating cell centers with a convolutional neural network(CNN) +1. Locating cell centers with a convolutional neural network(CNN) A convolutional neural network model was developed to automatically identify the location of the cell centers. The pipeline employed a sliding window approach for detection. That is , a small window slides across the entire image and for position output whether the position is the center of a cell or not. The training data was extracted and transformed from raw .csg files which are manually labeled by former researchers. Positive examples are obtained by generating a window centered on the center of the cell. Negative examples are obtained by random sampling outside the cells. @@ -28,4 +28,16 @@ For each image, the sliding window method predicts a set of points which are can         -###1.Detecting cell contour +1.Detecting cell contour +A dynamic programming algorithm was developed to detect the contour of single cell given a seed point at the center of the cell. +The principal algorithm is : +1) generate a series of rays of different direnctions from the seed of the cell detected, +2) compute several images which include pix_image, gradx, grady, grad_from_center... +3) get the values of each image on all points on the rays, which is named tab, pixtab, gxtab, gytab... +4) find out the optimal pathway(dynamic programming) through all of the rays which best represents the cell contour (manually defined scoring function) +5) filter the optimal pathway and get the polygon/mask of the cell + +Sample results: + + +