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电子科技公司网站网页设计,软件开发培训哪有,wordpress 过滤html代码,重庆最著名的十大景点Spatial Measures介绍空间转录组学和图像分析领域中#xff0c;研究人员试图回答的许多问题都与空间相关。观测值的坐标通常会缩放到当前使用的图像分辨率。以Visium平台为例#xff0c;如果将10X Visium输出中的tissue_lowres_image.png替换为tissue_hires_image.png#x…Spatial Measures介绍空间转录组学和图像分析领域中研究人员试图回答的许多问题都与空间相关。观测值的坐标通常会缩放到当前使用的图像分辨率。以Visium平台为例如果将10X Visium输出中的tissue_lowres_image.png替换为tissue_hires_image.png条形码斑点的坐标会相应缩放以确保坐标与图像保持对齐。因此坐标可用于回答相对空间问题但不能用于绝对度量。例如“坏死区域的面积约为400像素”这一说法是没有意义的。如果以像素为单位面积将始终取决于图像分辨率。本教程将解释SPATA2如何通过像素比例因子计算Visium平台从像素到SI单位的转换并提供关于如何利用SI距离进行工作的示例。library(SPATA2) library(tidyverse)# load SPATA2 inbuilt example data (and rename an image for this tutorial) object_t275 - loadExampleObject(UKF275T) %% renameImage(img_name image1, new_img_name lowres)text_size - theme(text element_text(size 17.5)) plotImage(object_t275, img_name lowres) text_size labs(subtitle Normal resolution)# very_low_res image has been registered using registerImage() plotImage(object_t275, img_name very_low_res) text_size labs(subtitle Very low resolution)2. 像素比例因子要以绝对数值回答问题必须将距离转换为国际单位制SI单位即微米、毫米、厘米等。这是可能的因为大多数空间组学研究都带有真实值。2.1 Visium在10X Visium的情况下此真实值是两个相邻条形码点之间的中心到中心距离该距离始终为100微米。利用此信息可通过像素比例因子计算实际距离和面积。该比例因子由initiateSpataObjectVisium()自动计算。如果您在SPATA2对象中注册了多张图像请注意默认情况下会使用活动图像的像素比例因子。# how many um is one pixel in side lengths getPixelScaleFactor(object_t275, unit um)## [1] 13.68328 ## attr(,unit) ## [1] um/px# how many pixel is one um in side lengths getPixelScaleFactor(object_t275, unit um, switch TRUE)## [1] 0.07308187 ## attr(,unit) ## [1] px/um# by default the pixel scale factor of the active image is used getImageNames(object_t275)## [1] lowres very_low_res# which is image lowres in this example activeImage(object_t275)## [1] lowres# how many um is one pixel in side lengths in case of an even lower resolution? getPixelScaleFactor(object_t275, unit um, img_name very_low_res)## [1] 78.94202 ## attr(,unit) ## [1] um/px2.2 MERFISH and Co像素比例因子这一术语源于SPATA2最初仅被认为适用于Visium数据集的时期。后来其应用范围已扩展到其他平台例如MERFISH该平台提供以微米为单位的细胞坐标。如果平台提供的观测坐标单位为国际单位制SI单位则理论上不需要像素比例因子。但为了使SPATA2代码正常运行SPATA2object中必须存在该比例因子。因此它会由相应的initiateSpataObject*()函数自动设置。例如在MERFISH数据中x坐标和y坐标以微米um为单位提供。因此通过initiateSpataObjectMERFISH()函数初始化的SPATA2对象的像素比例因子始终为1毫米/像素。3. 距离的运用多个函数的参数以某种方式涉及距离度量。SPATA2 使用 units 包来处理距离。除非文档中有其他说明否则可以将距离以像素或 SI 单位提供。在后台输入会被转换为像素并与当前分辨率对齐。4.1 距离转换部分给出了如何进行此操作的一些示例。3.1 处理距离输入和输出validUnitsOfLength()## nanometer micrometer millimeter centimeter decimeter meter pixel ## nm um mm cm dm m px# wrappers around units::set_units() as_micrometer(input 4mm)## 4000 [um]as_millimeter(input 4cm)## 40 [mm]### convert from si - pixel # example 1: a simple string works as_pixel(input 4mm, object object_t275)## [1] 292.3275 ## attr(,unit) ## [1] px# example 2: a unit object works, too unit_input - units::set_units(x 4, value mm) unit_input## 4 [mm]class(unit_input)## [1] unitsas_pixel(input unit_input, object object_t275)## [1] 292.3275 ## attr(,unit) ## [1] px### convert from pixel - si # example 1: simple numeric input is interpreted as pixel as_millimeter( input c(100, 200, 300), object object_t275 )## Units: [mm] ## [1] 1.368328 2.736657 4.104985# example 2: strings with px suffix work, too as_micrometer( input c(50px, 200px, 800px), object object_t275 )## Units: [um] ## [1] 684.1642 2736.6568 10946.62713.2 Examples以下是一些实际距离可能发挥作用的例子。# specifying x- and y-range while handling images xrange c(2.5mm, 6.5mm) yrange c(0.5mm, 4.5mm) # where to set the breaks is a measure of distance, too breaks - str_c(0:8, mm) # vector of valid distance inputs print(breaks)## [1] 0mm 1mm 2mm 3mm 4mm 5mm 6mm 7mm 8mmaxes_add_on - ggpLayerAxesSI(object_t275, unit mm, breaks breaks) rect_add_on - ggpLayerRect( object object_t275, xrange xrange, yrange yrange ) plotImage(object object_t275) rect_add_on axes_add_on text_sizeplotImage( object object_t275, xrange xrange, # crop the image with distance input yrange yrange # crop the image with distance input ) text_sizeplotImage(object_t275) ggpLayerAxesSI(object_t275, unit mm, breaks breaks) ggpLayerSpatAnnOutline(object_t275, ids img_ann_1, fill orange) ggpLayerHorizonSAS(object_t275, id img_ann_1, distance 1mm) ggpLayerScaleBarSI(object_t275, sb_dist 1mm, sb_pos c(5.5mm, 7.5mm), text_size 15, text_nudge_y 10) text_size4. 与区域相关的工作除了距离之外还可以计算面积。这在例如图像注释的面积与生物学问题相关时会变得有趣。4.1 处理区域输入和输出validUnitsOfArea()## [1] nm2 um2 mm2 cm2 dm2 m2 pxvalidUnitsOfAreaSI()## [1] nm2 um2 mm2 cm2 dm2 m2getPixelScaleFactor(object_t275, unit um2, img_name lowres)## [1] 187.2323 ## attr(,unit) ## [1] um2/px# more um2 per pixel in the very low resolution image # - pixels are smaller getPixelScaleFactor(object_t275, unit um2, img_name very_low_res)## [1] 6231.843 ## attr(,unit) ## [1] um2/px# numeric input is interpreted as pixel as_millimeter2(input c(200, 400, 4000, 50000), object object_t275)## Units: [mm^2] ## [1] 0.03744645 0.07489290 0.74892903 9.36161289# if character, different units can be specified as input as_centimeter2(input c(4mm2, 400px), object object_t275)## Units: [cm^2] ## [1] 0.040000000 0.0007489294.2 Examples# process the diet example object object_t313 - identifyTissueOutline(example_data$object_UKF313T_diet)# set ids of example spatial annotations ids - c(necrotic_area, necrotic_edge, necrotic_edge2) plotSpatialAnnotations(object_t313, ids ids, nrow 1)# process the diet example object object_mouse - loadExampleObject(LMU_MCI) object_mouse - identifyTissueOutline(object_mouse)# get tissue area by tisse section getTissueArea(object_mouse, unit mm2)## Units: [mm^2] ## tissue_section_1 tissue_section_2 ## 6.349445 7.945489getTissueArea(object_t313, unit mm2)## 29.67623 [mm^2]# left plotImage(object_t313, unit mm) ggpLayerTissueOutline(object_t313)# right plotImage(object_mouse, unit mm) ggpLayerTissueOutline(object_mouse)# use the three necrotic ids from above spat_ann_areas - getSpatAnnArea(object object_t313, ids ids, unit mm2) print(spat_ann_areas)## Units: [mm^2] ## necrotic_area necrotic_edge necrotic_edge2 ## 6.1849516 0.4618869 0.6252351threshold - units::set_units(x 1, value mm2) # keep only those with an area smaller than 1mm2 print(spat_ann_areas[spat_ann_areas threshold])## Units: [mm^2] ## necrotic_edge necrotic_edge2 ## 0.4618869 0.6252351