Additional file 1 of ImageJ2: ImageJ for the next generation of scientific image data

Figures and illustrations. Figure S1: Module execution in different contexts. When running a parameterized script (panel B) from the ImageJ user interface (panel A), a pop-up dialog box (panel C) enables the user to enter the name and age values; when running the script headless from the command line (panel D), input values are passed as arguments and output values echoed to the standard output stream. Figure S2: Comparison of time performance across ImageJ 1.x and ImgLib2 data structures. For ten iterations, we ran a “cheap” per-pixel operation and an “expensive” operation on a 25 Mpx image stored in the ImageJ 1.x container, various ImgLib2 containers, and raw byte arrays. Panel A (left) shows the time (ms) it took to complete a “cheap” operations versus the loop iteration for each container. Panel B (right) shows the same information but for the time (ms) it took to complete the expensive operation. Figure S3: Sample ImageJ plugin usage of ImageJ 1.x and ImageJ2. This plot displays a select few ImageJ plugins in varying stages of transition, from ImageJ 1.x to ImageJ2, as of 11 Aug 2017 2:35 PM CDT. The ratio of ImageJ 1.x to ImageJ2 usage was computed by counting the number of imports each plugin uses from relevant Java packages: "ImageJ 1.x plugins" is ij.plugin.*, "ImageJ 1.x data structures" is ij.* excluding the plugin subpackage, "SciJava framework" is org.scijava.*, and "ImageJ2 data structures" is net.imagej.* and net.imglib2.*. References for plugins shown: TrackMate [67], MaMuT [150], Multiview Reconstruction [70, 71], MotherMachine Analyzer (MoMA) [151, 152], Sholl Analysis [74], Kymograph Builder [153], Z-Spacing Correction [154], Trainable Weka Segmentation [155], Pendent Drop [156], SciView [157], BigDataViewer [66], Image Stitching [158], Coloc 2 [159], MorphoLibJ [100]. Table S1: Built-in SciJava input widgets. Table S2: Kinds and arities of special ops. Table S3: Image types supported by ImageJ. (ZIP 549 kb)

图件与插图。
图S1：不同上下文下的模块执行流程。当从ImageJ用户界面（图A）运行参数化脚本（图B）时，会弹出对话框（图C）供用户输入姓名与年龄参数值；当通过命令行以无头模式运行该脚本时（图D），输入值将以参数形式传入，输出值则回显至标准输出流。
图S2：ImageJ 1.x与ImgLib2数据结构的时间性能对比。针对存储于ImageJ 1.x容器、各类ImgLib2容器及原始字节数组中的25兆像素（25 Mpx）图像，我们执行了10次迭代的“轻量”逐像素操作与“耗时”操作。左图（图A）展示了各容器完成轻量操作的耗时（毫秒）与循环迭代次数的对应关系；右图（图B）则展示了各容器完成耗时操作的同类数据。
图S3：ImageJ 1.x与ImageJ2插件使用样例。本图表展示了截至2017年8月11日美国中部夏令时下午2点35分，处于从ImageJ 1.x向ImageJ2过渡不同阶段的多款ImageJ插件。我们通过统计各插件从相关Java包中导入的类数量，计算出二者的使用占比：其中“ImageJ 1.x插件”对应ij.plugin.*包，“ImageJ 1.x数据结构”对应除plugin子包外的ij.*包，“SciJava框架”对应org.scijava.*包，“ImageJ2数据结构”对应net.imagej.*与net.imglib2.*包。所展示插件的参考文献如下：TrackMate [67]、MaMuT [150]、Multiview Reconstruction（多视图重建）[70, 71]、MotherMachine Analyzer（MoMA，母机分析器）[151, 152]、Sholl Analysis（Sholl分析）[74]、Kymograph Builder（Kymograph构建器）[153]、Z-Spacing Correction（Z间距校正）[154]、Trainable Weka Segmentation（可训练Weka分割）[155]、Pendent Drop（悬滴分析）[156]、SciView [157]、BigDataViewer（大数据查看器）[66]、Image Stitching（图像拼接）[158]、Coloc 2 [159]、MorphoLibJ [100]。
表S1：内置SciJava输入小部件。
表S2：特殊算子的类型与元数。
表S3：ImageJ支持的图像类型。（ZIP格式，大小549 KB）