三维对象分析(MCIB3D)插件用户手册

3D Object Analysis (MCIB3D) - User Manual

Dragonfly Prototype Apps · 3D Object Analysis (MCIB3D)...

版本 Version 1.0 · 2026-07-09

第一部分 中文手册

目录

1. 简介

2. 适用场景

3. 安装与启用

4. 运行环境与首次配置

5. 界面说明

6. 使用步骤

7. 参数说明

8. 输出结果

9. 常见问题与故障排除

10. 注意事项与已知限制

11. 参考资料

1. 简介

三维对象分析(MCIB3D) 是一个 Dragonfly Prototype Apps 插件。它让你在 Dragonfly 中选择一个 Channel(图像通道) 或 二值 MultiROI,把它导出为 Fiji 可读取的 TIFF,再在本机安装的 Fiji/ImageJ 里调用 3D ImageJ Suite(MCIB3D) 执行 真三维(true-3D)对象分割、逐对象三维形状测量以及三维空间分布统计,最后把 Fiji 输出的三维标签图导入回 Dragonfly 生成一个 MultiROI,并在面板中显示逐对象测量表格(可另存为 CSV)。

与在单张切片上逐层处理不同,MCIB3D 直接在整个体数据上进行三维连通分析和三维分水岭分割,因此能正确处理跨切片相连的对象,并给出每个对象真正的三维体积、表面积和形状描述子。

底层引擎与算法

• 引擎: 3D ImageJ Suite(常简称 MCIB3D),作为 Fiji 的一个更新站点(update site)提供,更新站点名称为 mcib3d,地址为 https://sites.imagej.net/mcib3d/。
• 三维分割方法: 3D Simple Segmentation(阈值 + 三维连通标注)、3D Watershed(三维分水岭,可拆开相互接触的对象)、3D Spot Segmentation(针对亮斑/亮点的分割)。
• 三维几何测量: 通过 3D Manager 的 Measure3D 计算体积、表面积、致密度(compactness)、伸长度(elongation)等逐对象三维形状描述子。
• 三维空间统计: 通过 3D Manager 的距离分析计算对象之间的最近邻距离等空间分布统计。

许可证要点

3D ImageJ Suite(MCIB3D)采用 GPL-3.0-or-later 许可。本插件仅把它作为一个 独立的、无界面的 Fiji JVM 子进程 来驱动,通过 TIFF 与 CSV 文件交换数据,从不 把 MCIB3D 或 Fiji 的代码导入 Dragonfly 进程。这个子进程边界即为 GPL 隔离边界。插件本身不打包任何 Fiji 或 MCIB3D 代码,你需要在本机自行安装 Fiji。

2. 适用场景

本插件面向需要在 三维体数据 上做真三维对象分割、逐对象三维形貌统计与空间分布分析的用户。典型场景包括:

• 把相互接触/相连的三维对象(如孔隙、颗粒、气泡、细胞)拆开,并统计每个对象的体积与形状。
• 对分割后的每个对象计算三维形状描述子(体积、表面积、致密度、伸长度),用于形貌统计与分类。
• 分析对象之间的空间分布,例如计算每个对象到最近邻对象的距离,评估分散或聚集程度。
• 在材料学(CT 孔隙/颗粒/气泡)、生命科学(细胞、细胞核、斑点)等领域,把 Dragonfly 的可视化能力与 MCIB3D 成熟的三维对象分析算法结合起来。

本插件只处理 已存在 的 Dragonfly Channel 或二值 MultiROI,它不会替你创建源对象。请先在 Dragonfly 中准备好要分析的图像通道或二值分割结果。

3. 安装与启用

本插件随 Prototype Labs & Apps 完整安装包(Full Package) 分发。安装步骤如下:

1. 把完整安装包 zip 解压到任意 较短 的目录(例如 C:\PL\),避免放在很深的下载目录或 OneDrive 重定向的桌面下。

2. 双击运行 `Install_FullPackage.bat`。

3. 在弹出的对话框中选择核心安装模式(Fresh 全新安装 / Compatible 兼容安装),然后在应用列表中 勾选 “3D Object Analysis (MCIB3D)...”。

4. 点击 Install,等待控制台完成。

5. 完全退出并重启 Dragonfly(菜单只在 Dragonfly 启动时被扫描发现)。

本插件在完整安装包中 默认不勾选(default disabled)。你必须在安装器里手动勾选它,或稍后在 Menu Item Manager 中启用,重启后才会出现在菜单里。

重启后,菜单项出现在:Prototype Apps ▸ 3D Object Analysis (MCIB3D)...(位于 “Measurements & Analysis(测量与分析)” 分组中)。点击它会打开一个可停靠的面板。

以后修改勾选

最方便的方式是在 Dragonfly 里改:打开 Developer ▸ Prototype Labs... ▸ Menu Item Manager,在底部的 “Prototype Apps (Full Package)” 列表中找到本插件的复选框,勾选=部署,取消=移除菜单项,重启 Dragonfly 生效。停用 从不 删除已配置的 Fiji 路径或本机 Fiji 安装。你也可以随时重跑安装器,它会记住上次的勾选作为默认值。

卸载

双击 `Uninstall_FullPackage.bat` 即可移除所有 Full Package 的菜单项与插件。卸载不会删除你本机的 Fiji 安装或 MCIB3D 更新站点。

4. 运行环境与首次配置

本插件 不创建任何 Python 虚拟环境(venv),不使用 GPU,也不需要 WSL。它唯一的外部依赖是 本机安装的 Fiji/ImageJ,并在其中启用了 3D ImageJ Suite(MCIB3D) 更新站点。

第 1 步:准备 Fiji

如果你尚未安装 Fiji,请先从 Fiji 官网(fiji.sc)下载并解压 Fiji。插件会在常见位置自动查找 Fiji 启动器(例如 Fiji.app、Fiji、ImageJ 目录),识别的启动器文件名包括 ImageJ-win64.exe、fiji-windows-x64.exe、fiji.exe、ImageJ-win32.exe、ImageJ.exe 等。

第 2 步:指定 Fiji 启动器

打开面板后,在 “Fiji / 3D ImageJ Suite (MCIB3D)” 分组里:

• 点击 Locate 让插件自动查找 Fiji;若找到,路径会自动填入 Launcher(启动器) 输入框,状态栏会提示是否检测到 MCIB3D。
• 若自动查找失败,点击 Browse... 手动选择 Fiji 启动器(如 ImageJ-win64.exe 或 fiji-windows-x64.exe)。
• 也可以通过环境变量 DF_FIJI_PATH 预先指定 Fiji 启动器路径。

若你选择的是 Jaunch 版启动器(fiji-windows-x64.exe 等),插件会在同目录下优先使用经典的 ImageJ-win64.exe 启动器,因为它的无界面 -batch 行为最稳定。

第 3 步:检查 / 安装 MCIB3D(需联网)

点击 “Check / Install 3D ImageJ Suite (MCIB3D)” 按钮。插件会扫描所选 Fiji 安装的 plugins、jars 等目录,查找文件名含 mcib3d 等关键字的 jar 文件:

• 已检测到: 弹窗提示 MCIB3D 的路径,状态栏显示 “MCIB3D detected”。
• 未检测到: 弹出确认框询问是否现在启用 mcib3d 更新站点。确认 Yes 后,插件会以无界面方式运行 Fiji 的更新器命令,添加更新站点 mcib3d(https://sites.imagej.net/mcib3d/)并应用更新。

安装/更新 MCIB3D 需要联网,可能耗时几分钟。安装完成后,通常需要重启 Fiji/Dragonfly 才能让新命令生效——若安装结束后按文件扫描仍未检测到 MCIB3D,请重启后再试,或在 Fiji 里通过 Help ▸ Update ▸ Manage update sites ▸ 3D ImageJ Suite 手动启用。正常的图像处理(非安装)不需要联网。

设置 JVM 内存(Max heap)

Max heap(最大堆内存) 决定分配给 Fiji JVM 子进程的内存,默认为 4096 MB。处理较大的三维体数据时,请把它设得足够大(与你机器可用内存相匹配),否则 Fiji 可能因内存不足而失败。设为 0 表示不传递 --mem 参数,使用 Fiji 默认值。

面板设置(Fiji 路径、Max heap、MultiROI 后缀)会保存在插件代码目录的 mcib3d_config.json 中,下次打开自动恢复。

5. 界面说明

面板从上到下依次为以下区域:

顶部说明

一段简介文字,说明本插件用 Fiji 的 3D ImageJ Suite 对 Dragonfly Channel 或二值 MultiROI 执行真三维分割、逐对象三维形状描述子和三维空间统计,并导入三维标签 MultiROI 与测量表格。

Input(Channel 或二值 MultiROI)

• 下拉框: 列出当前 Dragonfly 场景里可用的 Channel 与 MultiROI;每项后面标注类型([Channel ...] / [MultiROI ...])和尺寸(Z×Y×X)。若有当前选中的对象会优先列出。
• Refresh: 重新扫描并刷新可选输入列表。

MCIB3D operation(操作)

• 操作下拉框: 三个操作可选 —— 3D Segmentation -> labels(三维分割)、3D Geometrical Measure(三维几何测量)、3D Spatial Statistics(三维空间统计)。
• 动态参数区: 根据所选操作显示对应的参数控件(见第 7 章),下方的灰色说明文字会随操作切换而更新。

Fiji / 3D ImageJ Suite (MCIB3D)

• Launcher(启动器)输入框 + Locate + Browse...: Fiji/ImageJ 启动器路径;Locate 自动查找,Browse 手动选择。
• Max heap(最大堆内存)微调框: Fiji JVM 最大内存,单位 MB,默认 4096,步进 512,范围 0–262144。
• Check / Install 3D ImageJ Suite (MCIB3D) 按钮: 检测所选 Fiji 是否装有 MCIB3D,未装则询问是否启用更新站点安装。

Output(输出)

MultiROI suffix(MultiROI 后缀)输入框: 输出对象命名后缀,默认 MCIB3D。最终 MultiROI 名称为 <输入对象名> - <后缀>。

运行按钮与结果区

• Run MCIB3D + Create MultiROI(蓝色按钮): 执行整个工作流。
• 测量结果表格: 对于测量/空间统计操作,运行后显示逐对象/逐对的结果表(默认隐藏,有结果时显示)。
• Save measurements as CSV... 按钮: 把表格另存为 CSV 文件(有结果时显示)。
• 状态栏 + 日志窗口: 状态栏显示一句话进度/结果;下方只读日志窗口显示详细过程,包括 Fiji 输出、临时任务文件夹路径以及出错信息。

6. 使用步骤

下面是从输入到输出的完整端到端流程。

1. 在 Dragonfly 中准备好要分析的 Channel 或 二值 MultiROI。

2. 打开面板:Prototype Apps ▸ 3D Object Analysis (MCIB3D)...。

3. 在 Input 下拉框中选择输入对象(如没看到,点 Refresh 刷新)。

4. 在 MCIB3D operation 下拉框选择操作,并在下方参数区设置阈值、最小/最大尺寸、连通性等参数(见第 7 章)。

5. 在 Fiji 分组里确认 Launcher 已指向有效的 Fiji 启动器(必要时用 Locate/Browse),并按需调整 Max heap。

6. 首次使用点击 Check / Install 3D ImageJ Suite (MCIB3D) 确认已安装 MCIB3D(未装则按提示安装并重启)。

7. 在 Output 里设置 MultiROI suffix(可保持默认 MCIB3D)。

8. 点击 Run MCIB3D + Create MultiROI。插件会把输入导出为 ImageJ TIFF、无界面运行 Fiji 宏、把三维标签 TIFF 导入回 Dragonfly 生成 MultiROI,并显示测量表格(若该操作产生表格)。

9. 查看日志中的 “Created MultiROI ... with N label(s)” 与任务文件夹路径;若有表格,可点 Save measurements as CSV... 导出。

各操作的输入要求与产出

• 3D Segmentation -> labels: 输入通常是一个 Channel(保留强度值以便阈值分割),按所选方法(简单分割 / 分水岭 / 亮斑分割)得到三维标签 → MultiROI。
• 3D Geometrical Measure: 输入 Channel 或二值 MultiROI,先做三维简单分割标注,再逐对象计算体积、表面积、致密度、伸长度 → MultiROI + 逐对象测量表格。
• 3D Spatial Statistics: 输入 Channel 或二值 MultiROI,先标注,再计算对象间的最近邻距离等空间分布统计 → MultiROI + 最近邻距离表格。

二值 MultiROI 会被导出为 0/255 掩膜;Channel 则保留强度值(浮点数据会被拉伸到 16 位范围),这样阈值参数才有意义。

7. 参数说明

3D Segmentation -> labels(三维分割) 的参数:

3D Geometrical Measure(三维几何测量) 与 3D Spatial Statistics(三维空间统计) 的参数(两者相同):

Fiji / 输出相关设置:

8. 输出结果

运行完成后,插件会在 Dragonfly 中生成以下结果:

• MultiROI(三维标签): 由 Fiji 输出的三维标签 TIFF 转换而来,标签被重新编号(1..N),几何信息(体素间距、原点)尽量沿用源对象。MultiROI 会自动分配默认颜色并发布(publish)到场景,可在 Dragonfly 对象树中查看,并在 2D/3D 视图中显示各个对象。
• 逐对象测量表格(仅测量/空间统计操作): 在面板中以表格显示。三维几何测量给出每个对象的体积、表面积、致密度、伸长度等;三维空间统计给出每个对象的最近邻距离等。点击 Save measurements as CSV... 可另存为 CSV。

中间文件(输入 TIFF、标签 TIFF、结果 CSV、宏文件)保存在操作系统临时目录下的一个任务文件夹中(日志会打印该路径,形如 mcib3d_*)。运行失败时,这些临时路径会保留在错误信息里,方便你在 Fiji 中手动检查。

导入回 Dragonfly 的 MultiROI 最多支持 65535 个标签(uint16)。若分割出的对象数超过此上限,导入会报错——请通过提高阈值或增大最小尺寸来减少对象数量。

9. 常见问题与故障排除

问:菜单里找不到 “3D Object Analysis (MCIB3D)...”?

答:本插件默认不勾选。请在完整安装包安装器里勾选它,或在 Developer ▸ Prototype Labs... ▸ Menu Item Manager 中启用,然后 完全重启 Dragonfly(菜单只在启动时被发现)。

问:提示找不到 Fiji / 启动器未设置?

答:先安装 Fiji;然后在面板中点 Locate 自动查找,或点 Browse... 手动选择 ImageJ-win64.exe / fiji-windows-x64.exe;也可用环境变量 DF_FIJI_PATH 指定。

问:安装 MCIB3D 后仍检测不到,或运行时提示某个命令不可用?

答:MCIB3D 更新站点安装后通常需要 重启 Fiji/Dragonfly 才能加载新 jar。若仍检测不到,可在 Fiji 里通过 Help ▸ Update ▸ Manage update sites ▸ 3D ImageJ Suite 手动启用更新站点,应用更新并重启。注意不同 Fiji 版本的 MCIB3D 命令名/选项可能略有差异,遇到命令不可用时请查看日志里的 Fiji 输出。

问:运行很慢或因内存不足失败?

答:三维数据在外部 Fiji 进程中处理,较大的体数据会耗时较长并需要足够的 JVM 堆内存。请把 Max heap 调大到与机器可用内存相匹配;必要时先裁剪数据或提高最小尺寸阈值以减少对象数。

问:运行成功但没有生成 MultiROI 或表格为空?

答:通常是阈值/尺寸参数导致没有前景对象。请降低 Threshold (low) 或 Min size,并确认输入对象确实包含目标结构。日志会打印任务文件夹路径,可在其中检查 Fiji 生成的中间文件。

10. 注意事项与已知限制

• 本插件只处理 已存在 的 Dragonfly Channel 或二值 MultiROI,不会替你创建源对象。
• Fiji/MCIB3D 操作作为 外部进程 运行,大体数据可能较慢并需要足够的 JVM 堆内存。
• 输出 MultiROI 的几何信息尽量从源对象恢复;导入的标签数受 uint16 上限(65535)约束。
• 不同 Fiji 版本中 MCIB3D 的命令名与选项可能不同;本插件采用当前 3D ImageJ Suite 的标准命令名,当命令不可用时会在日志中报告 Fiji 的 stdout/stderr。
• MCIB3D 为 GPL-3.0-or-later,仅作为独立的无界面 Fiji JVM 子进程被驱动,不会导入 Dragonfly 进程;插件不打包任何 Fiji/MCIB3D 代码,需要你自行安装 Fiji。
• 安装/更新 MCIB3D 需要联网;正常的图像处理不需要联网、GPU 或 WSL,也不创建 Python 虚拟环境。

11. 参考资料

• Fiji(ImageJ 发行版)官网:https://fiji.sc/
• 3D ImageJ Suite(MCIB3D)Fiji 更新站点:https://sites.imagej.net/mcib3d/
• 3D ImageJ Suite 文档(mcib3d):可在其项目页与 Fiji 内的 3D Manager 帮助中查阅。
• 许可证:3D ImageJ Suite(MCIB3D)为 GPL-3.0-or-later。

Part II English Manual

Contents

1. Overview

2. Use Cases

3. Installation and Enabling

4. Environment and First-Run Setup

5. Interface Reference

6. Step-by-Step Usage

7. Parameter Reference

8. Outputs

9. FAQ and Troubleshooting

10. Notes and Known Limitations

11. References

1. Overview

3D Object Analysis (MCIB3D) is a Dragonfly Prototype Apps plugin. It lets you pick a Dragonfly Channel or binary MultiROI, export it as a Fiji-readable TIFF, then run the 3D ImageJ Suite (MCIB3D) inside your locally-installed Fiji/ImageJ to perform true-3D object segmentation, per-object 3D shape measurements, and 3D spatial-distribution statistics. The resulting 3D label image is imported back into Dragonfly as a MultiROI, and a per-object measurements table is shown in the panel (savable as CSV).

Unlike slice-by-slice processing, MCIB3D works directly on the whole volume with 3D connectivity and 3D watershed, so it correctly handles objects that span slices and reports each object's true 3D volume, surface area and shape descriptors.

Underlying engine and algorithms

• Engine: the 3D ImageJ Suite (commonly abbreviated MCIB3D), provided as a Fiji update site named mcib3d at https://sites.imagej.net/mcib3d/.
• 3D segmentation methods: 3D Simple Segmentation (threshold + 3D connected labelling), 3D Watershed (splits touching objects), 3D Spot Segmentation (tuned for bright blobs/spots).
• 3D geometrical measure: per-object 3D descriptors (volume, surface area, compactness, elongation) via the 3D Manager Measure3D command.
• 3D spatial statistics: inter-object spatial distribution such as nearest-neighbour distances via the 3D Manager distance analysis.

Licensing

The 3D ImageJ Suite (MCIB3D) is licensed GPL-3.0-or-later. This plugin drives it only as a separate, headless Fiji JVM subprocess, exchanging data through TIFF and CSV files, and never imports MCIB3D or Fiji code into the Dragonfly process. That subprocess boundary is the GPL isolation boundary. The plugin bundles no Fiji or MCIB3D code; you install Fiji yourself.

2. Use Cases

This plugin targets users who need true-3D object segmentation, per-object 3D morphometry, and spatial-distribution analysis on volumetric data. Typical scenarios:

• Split touching/connected 3D objects (pores, grains, bubbles, cells) and report each object's volume and shape.
• Compute per-object 3D shape descriptors (volume, surface area, compactness, elongation) for morphometric statistics and classification.
• Analyse spatial distribution, e.g. each object's distance to its nearest neighbour, to assess dispersion or clustering.
• Combine Dragonfly's visualization with the mature 3D object-analysis algorithms of MCIB3D in materials science (CT pores/grains/bubbles) and life sciences (cells, nuclei, spots).

The plugin only processes an existing Dragonfly Channel or binary MultiROI; it does not create the source object for you. Prepare the image Channel or binary segmentation in Dragonfly first.

3. Installation and Enabling

This plugin ships in the Prototype Labs & Apps Full Package. To install:

1. Unzip the Full Package to any short folder (e.g. C:\PL\); avoid deep Downloads paths or a OneDrive-redirected Desktop.

2. Double-click `Install_FullPackage.bat`.

3. In the dialog, pick the core install mode (Fresh or Compatible), then tick "3D Object Analysis (MCIB3D)..." in the app list.

4. Click Install and wait for the console to finish.

5. Fully quit and restart Dragonfly (menus are discovered only at Dragonfly startup).

This plugin is disabled by default in the Full Package. You must tick it in the installer, or enable it later in the Menu Item Manager, and restart before it appears in the menu.

After the restart, the menu item appears under Prototype Apps ▸ 3D Object Analysis (MCIB3D)... (in the "Measurements & Analysis" group). Clicking it opens a dockable panel.

Changing your choice later

The easiest way is inside Dragonfly: open Developer ▸ Prototype Labs... ▸ Menu Item Manager, find this plugin's checkbox in the "Prototype Apps (Full Package)" list, tick to deploy / untick to remove the menu entry, and restart Dragonfly to apply. Disabling never deletes your configured Fiji path or your local Fiji install. You may also re-run the installer at any time; it remembers your previous choices as defaults.

Uninstall

Double-click `Uninstall_FullPackage.bat` to remove all Full-Package menu items and plugins. Uninstalling does not delete your local Fiji install or the MCIB3D update site.

4. Environment and First-Run Setup

This plugin creates no Python virtual environment (venv), uses no GPU, and needs no WSL. Its only external dependency is a locally-installed Fiji/ImageJ with the 3D ImageJ Suite (MCIB3D) update site enabled.

Step 1: Have Fiji installed

If you do not yet have Fiji, download and unzip it from the Fiji website (fiji.sc). The plugin auto-searches common locations (e.g. Fiji.app, Fiji, ImageJ folders); recognised launcher names include ImageJ-win64.exe, fiji-windows-x64.exe, fiji.exe, ImageJ-win32.exe, and ImageJ.exe.

Step 2: Point the panel at the Fiji launcher

In the "Fiji / 3D ImageJ Suite (MCIB3D)" group of the panel:

• Click Locate to auto-detect Fiji; if found, the path is filled into the Launcher field and the status line reports whether MCIB3D was detected.
• If auto-detection fails, click Browse... to select the Fiji launcher (e.g. ImageJ-win64.exe or fiji-windows-x64.exe).
• You may also pre-set the launcher path via the DF_FIJI_PATH environment variable.

If you select a Jaunch launcher (e.g. fiji-windows-x64.exe), the plugin prefers the classic ImageJ-win64.exe launcher in the same folder because its headless -batch behaviour is the most reliable.

Step 3: Check / install MCIB3D (needs internet)

Click "Check / Install 3D ImageJ Suite (MCIB3D)". The plugin scans the selected Fiji install's plugins, jars (and related) folders for jar files whose names contain mcib3d and similar tokens:

• Detected: a dialog reports the MCIB3D path and the status line shows "MCIB3D detected".
• Not detected: a confirmation dialog asks whether to enable the mcib3d update site now. On Yes, the plugin runs Fiji's updater commands headlessly to add the mcib3d update site (https://sites.imagej.net/mcib3d/) and apply updates.

Installing/updating MCIB3D needs internet and may take a few minutes. After it finishes you usually must restart Fiji/Dragonfly for the new commands to load. If the file scan still does not find MCIB3D after install, restart and try again, or enable it manually in Fiji via Help ▸ Update ▸ Manage update sites ▸ 3D ImageJ Suite. Normal processing (not install) needs no internet.

Setting JVM memory (Max heap)

Max heap sets the memory given to the Fiji JVM subprocess; the default is 4096 MB. For large volumes, set it high enough to match your machine's available RAM, or Fiji may fail out of memory. 0 passes no --mem flag and uses Fiji's default.

Panel settings (Fiji path, Max heap, MultiROI suffix) are saved in mcib3d_config.json in the plugin's code folder and restored next time you open the panel.

5. Interface Reference

The panel is laid out top-to-bottom as follows.

Intro

A short description stating that the plugin runs true-3D segmentation, per-object 3D shape descriptors, and 3D spatial statistics on a Dragonfly Channel or binary MultiROI with the 3D ImageJ Suite in Fiji, and imports a 3D label MultiROI plus a measurements table.

Input (Channel or binary MultiROI)

• Dropdown: lists the Channels and MultiROIs available in the current Dragonfly scene; each item is tagged with its type ([Channel ...] / [MultiROI ...]) and shape (Z×Y×X). Currently-selected objects are listed first.
• Refresh: rescans and refreshes the input list.

MCIB3D operation

• Operation dropdown: three operations — 3D Segmentation -> labels, 3D Geometrical Measure, and 3D Spatial Statistics.
• Dynamic parameter area: shows the parameter widgets for the selected operation (see Chapter 7); a grey description line updates as you switch operations.

Fiji / 3D ImageJ Suite (MCIB3D)

• Launcher field + Locate + Browse...: the Fiji/ImageJ launcher path; Locate auto-detects, Browse selects manually.
• Max heap spinbox: the Fiji JVM maximum memory in MB, default 4096, step 512, range 0–262144.
• Check / Install 3D ImageJ Suite (MCIB3D) button: detects whether MCIB3D is present in the selected Fiji and, if not, offers to enable the update site.

Output

MultiROI suffix field: the output naming suffix, default MCIB3D. The final MultiROI name is <input title> - <suffix>.

Run button and results area

• Run MCIB3D + Create MultiROI (blue button): runs the full workflow.
• Measurements table: for measure / spatial-statistics operations, shows the per-object/per-pair results after a run (hidden by default; shown when results exist).
• Save measurements as CSV... button: exports the table to a CSV file (shown when results exist).
• Status line + log: the status line shows a one-line progress/result; the read-only log below shows detailed progress, Fiji output, the temporary job folder path, and any errors.

6. Step-by-Step Usage

Here is the complete end-to-end flow from input to output.

1. In Dragonfly, prepare the Channel or binary MultiROI to analyse.

2. Open the panel: Prototype Apps ▸ 3D Object Analysis (MCIB3D)....

3. In the Input dropdown, select the input object (click Refresh if it is not listed).

4. In MCIB3D operation, choose the operation and set threshold, min/max size, and connectivity below (see Chapter 7).

5. In the Fiji group, confirm Launcher points at a valid Fiji launcher (use Locate/Browse if needed) and adjust Max heap as required.

6. On first use, click Check / Install 3D ImageJ Suite (MCIB3D) to confirm MCIB3D is installed (install and restart if prompted).

7. In Output, set the MultiROI suffix (the default MCIB3D is fine).

8. Click Run MCIB3D + Create MultiROI. The plugin exports the input to an ImageJ TIFF, runs the Fiji macro headlessly, imports the 3D label TIFF back into Dragonfly as a MultiROI, and shows a measurements table (if the operation produces one).

9. Check the log for "Created MultiROI ... with N label(s)" and the job folder path; if a table is present, click Save measurements as CSV... to export it.

Input requirements and outputs per operation

• 3D Segmentation -> labels: input is typically a Channel (intensities kept for thresholding); the chosen method (simple / watershed / spot) produces a 3D label image → MultiROI.
• 3D Geometrical Measure: input is a Channel or binary MultiROI; it is 3D-simple-segmented first, then per-object volume, surface area, compactness and elongation are computed → MultiROI + per-object table.
• 3D Spatial Statistics: input is a Channel or binary MultiROI; it is labelled first, then inter-object nearest-neighbour distances and related statistics are computed → MultiROI + nearest-neighbour table.

A binary MultiROI is exported as a 0/255 mask; a Channel keeps its intensities (float data is scaled to the 16-bit range) so the threshold parameters remain meaningful.

7. Parameter Reference

Parameters for 3D Segmentation -> labels:

Parameters for 3D Geometrical Measure and 3D Spatial Statistics (identical):

Fiji / output settings:

8. Outputs

After a run, the plugin produces the following in Dragonfly:

• MultiROI (3D labels): converted from the Fiji 3D label TIFF, with labels renumbered 1..N and geometry (voxel spacing, origin) restored from the source object where possible. The MultiROI is assigned default colours and published to the scene, visible in the Dragonfly object tree and in the 2D/3D views.
• Per-object measurements table (measure / spatial-statistics operations only): shown as a table in the panel. 3D geometrical measure reports each object's volume, surface area, compactness, elongation, etc.; 3D spatial statistics reports each object's nearest-neighbour distance, etc. Click Save measurements as CSV... to export it.

Intermediate files (input TIFF, label TIFF, results CSV, macro file) are written to a job folder under the OS temp directory (the log prints the path, of the form mcib3d_*). On failure, these temp paths are kept in the error text so you can inspect the Fiji output manually.

The imported MultiROI supports at most 65535 labels (uint16). If segmentation yields more objects than that, the import fails — reduce the object count by raising the threshold or increasing the minimum size.

9. FAQ and Troubleshooting

Q: I can't find "3D Object Analysis (MCIB3D)..." in the menu.

A: The plugin is disabled by default. Tick it in the Full Package installer, or enable it in Developer ▸ Prototype Labs... ▸ Menu Item Manager, then fully restart Dragonfly (menus are discovered only at startup).

Q: It says Fiji was not found / the launcher is not set.

A: Install Fiji first; then click Locate to auto-detect, or Browse... to select ImageJ-win64.exe / fiji-windows-x64.exe; you can also set the DF_FIJI_PATH environment variable.

Q: MCIB3D is still not detected after installing, or a command is reported as unavailable at run time.

A: After the mcib3d update site is installed you usually must restart Fiji/Dragonfly to load the new jars. If it is still not detected, enable the update site manually in Fiji via Help ▸ Update ▸ Manage update sites ▸ 3D ImageJ Suite, apply updates and restart. MCIB3D command names/options can differ between Fiji builds; if a command is unavailable, check the Fiji output in the log.

Q: Runs are slow or fail out of memory.

A: 3D data is processed in an external Fiji process; large volumes take time and need enough JVM heap. Raise Max heap to match your machine's available RAM; if needed, crop the data first or raise the minimum-size threshold to reduce the object count.

Q: The run succeeded but no MultiROI was created or the table is empty.

A: This usually means the threshold/size parameters left no foreground objects. Lower Threshold (low) or Min size, and confirm the input object actually contains the target structures. The log prints the job folder path so you can inspect the Fiji intermediate files.

10. Notes and Known Limitations

• The plugin only processes an existing Dragonfly Channel or binary MultiROI; it does not create the source object for you.
• Fiji/MCIB3D operations run as an external process, so large volumes can be slow and need enough JVM heap.
• The output MultiROI's geometry is restored from the source object where possible; the number of imported labels is bounded by the uint16 limit (65535).
• MCIB3D command names and options can vary between Fiji builds; the plugin uses standard command names from current 3D ImageJ Suite installs and reports Fiji stdout/stderr in the log when a command is unavailable.
• MCIB3D is GPL-3.0-or-later, driven only as a separate headless Fiji JVM subprocess and never imported into Dragonfly; the plugin bundles no Fiji/MCIB3D code — you install Fiji yourself.
• Installing/updating MCIB3D needs internet; normal processing needs no internet, GPU or WSL, and creates no Python virtual environment.

11. References

• Fiji (the ImageJ distribution): https://fiji.sc/
• 3D ImageJ Suite (MCIB3D) Fiji update site: https://sites.imagej.net/mcib3d/
• 3D ImageJ Suite documentation (mcib3d): available on its project page and in the 3D Manager help within Fiji.
• License: the 3D ImageJ Suite (MCIB3D) is GPL-3.0-or-later.