## ----style, echo=FALSE, results='asis'-------------------------------------------------- BiocStyle::latex() ## ----eval=FALSE------------------------------------------------------------------------- # source("https://bioconductor.org/biocLite.R") # biocLite("MaxContrastProjection") ## --------------------------------------------------------------------------------------- library(MaxContrastProjection) library(EBImage) data(cells) dim(cells) ## --------------------------------------------------------------------------------------- max_contrast = contrastProjection(imageStack = cells, w_x = 15, w_y = 15, smoothing = 5, brushShape = "box") ## --------------------------------------------------------------------------------------- max_contrast_large = contrastProjection(imageStack = cells[30:95, 55:115,], w_x = 15, w_y = 15, smoothing = 5, brushShape = "box") max_contrast_small = contrastProjection(imageStack = cells[30:95, 55:115,], w_x = 3, w_y = 3, smoothing = 5, brushShape = "box") ## ----echo=FALSE------------------------------------------------------------------------- display(max_contrast_large / max(cells), method = "raster") ## ----echo=FALSE------------------------------------------------------------------------- display(max_contrast_small / max(cells), method = "raster") ## --------------------------------------------------------------------------------------- contrastStack = getContrastStack(imageStack = cells, w_x = 15, w_y = 15, brushShape = "box") indexMap = getIndexMap(contrastStack = contrastStack, smoothing = 5) max_contrast_fromMap = projection_fromMap(imageStack = cells, indexMap = indexMap) ## --------------------------------------------------------------------------------------- max_intensity_proj = intensityProjection(imageStack = cells, projType = "max") min_intensity_proj = intensityProjection(imageStack = cells, projType = "min") mean_intensity_proj = intensityProjection(imageStack = cells, projType = "mean") median_intensity_proj = intensityProjection(imageStack = cells, projType = "median") sd_intensity_proj = intensityProjection(imageStack = cells, projType = "sd") sum_intensity_proj = intensityProjection(imageStack = cells, projType = "sum") ## ----sessioninfo, results='asis'-------------------------------------------------------- toLatex(sessionInfo())