## ----style, eval=TRUE, echo=FALSE, results="asis"-------------------------- BiocStyle::乳胶（）## ----设置，include = false ---------------------------------------------------------------------------------------------------------------------------------------------------库（knitr）opts_chunk $ set（figpath =“ figexamplesementation/”，fig.show =“ hold”，fig.align =“中心”，out.width=“ 0.35 \\ lineWidth”）## ------------- true，inclage = false -------------------------------------------------------------------------------------------------------------------------------库（Furrowseg）## ----消息= false -------------------------------------------------------------------------------------------------------------------------------------数据（“ examplefurrowmovie”）img < - examplefurrowmovie rm（examplefurnowmovie）## ---- segparm ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 0.0005 px <-0.293 filtersize <-sakeodd（rough（microns2px（1，px = px））））l < - makeodd（圆形（microns2px（5，px = px）））minObjectsize <-aind2px（4，px = px）maxObjectsize <-Aring2px（400，px = px）## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ z <- makeBrush(size =过滤，shape =“高斯”，sigma = filttersize/2）显示（strumanize（img [，，1，100]），method =“ raster”）img2 <-filter2（img，z）display（normanize（img2 [，，1，100]），方法=“ raster”）## ----适应性抢劫-----------------------------------------------------------------------------------------------------------------------------------------------------------------蒙版<-thresh（x = img2 [，1，]，w = l/2，h = l/2，offset = threshshoffset）display（mask [，，100]，method =“ raster”）## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- brush <- makeBrush(size=filterSize, shape="disc") mask <- closing(mask, brush) mask <- bwlabel(mask) mask <- furrowSeg::: filterObjects（mask，minobjectsize，inf）显示（掩码[，100]，method =“ raster”）## ----------------------------------------------------------------------------------------------------------------------------------- mask <- furrowSeg:::invertMask(mask) mask <- fillHull(mask) mask <- furrowSeg:::filterObjects(mask, 0, maxObjectSize) display(mask[, , 100], method="raster") ## ----propagateSegmentation------------------------------------------------- mask <- reenumerate(mask) mask <- propagate(img2[, , 1, ], seeds=mask) mask <- furrowSeg:::filterObjects(mask, minObjectSize, maxObjectSize) hs <- paintObjects(x=mask, tgt=normalize(img), col="yellow") display(hs[, , 1, 100], method="raster") ## ----comparisonToPackageFunction------------------------------------------- x <- segmentFurrowAllStacks(x=img, L=L, filterSize=filterSize, threshOffset=threshOffset, closingSize=filterSize, minObjectSize=minObjectSize, maxObjectSize=maxObjectSize) all(mask == x$mask[[1]]) ## ----featureExtraction----------------------------------------------------- nt <- dim(mask)[3] getEBImageFeatures <- function(mask, ref) { xbw <- reenumerate(mask) fts <- computeFeatures(x=xbw, ref=ref, methods.noref=c("computeFeatures.moment", "computeFeatures.shape")) return(fts) } ftList <- lapply(1:nt, function(t) { df <- getEBImageFeatures(mask[, , t], img[, , 1, t]) df <- as.data.frame(df, stringsAsFactors=FALSE) df$t <- t return(df) }) fts <- do.call("rbind", ftList) ## ----APanisotropy---------------------------------------------------------- fts$e.x <- cos(fts$x.0.m.theta)*fts$x.0.m.eccentricity ## ----plotFeatures, out.width="0.5\\linewidth"------------------------------ box <- c("xleft"=64, "xright"=448, "ybottom"=128, "ytop"=384) fts <- isolateBoxCells(fts, box) plotFeatureEvolution(fts, tMax=10, dt=4.22/60, px=0.293)