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+---
+title: nnInterAppose 
+description: Plugin to use nnInteractive from Fiji relying on Appose.
+source-url: https://github.com/Image-Analysis-Hub/nnInterappose
+icon: /media/icons/nninteractive.png
+license: BSD-3 Clause license
+categories: [Segmentation, Annotation]
+forum-tag: ""
+dev-status: 'active'
+update-site: 'Appose-Playground'
+team-founder: ["Gaelle Letort"]
+team-maintainer: ["Gaelle Letort"]
+team-developers: ["Gaelle Letort"]
+---
+
+This plugin install and run [nnInteractive]([https://www.cellpose.org/](https://github.com/MIC-DKFZ/nnInteractive)) on a stack (3D) in Fiji. 
+nnInteractive segments objects in 3D based on prompts placed by the user.
+
+This plugin is based on [Appose](https://github.com/apposed/appose), that automatically install python environment and allows python script execution with shared objects with Fiji.
+
+## Installation
+
+You can install the plugin for the unliste update site `Appose-Playground`:
+- In Fiji, go to `Help>Update...`
+- Select `Manage Update Sites` in the window that opens.
+- Click `Add unliste update site`, name it `Appose-Playground` and write its address `https://sites.imagej.net/Appose-Playground`.
+- Select the nnInterappose `.jar` file to install only this plugin, or keep all proposed plugins. 
+- Press `Apply changes` and restart Fiji when it's done.
+
+{% include notice icon="warning" content=" You should have a recent version of Fiji, based on Java 21 or more. Download a new version [here (Latest downloads column)](https://imagej.net/software/fiji/downloads) if you're current installation is too old." %}
+
+## Usage
+
+### Image dimensions
+The image must be a 3D (Z slices or T frames) image.
+It does not support 2D image or 3D+time stacks.
+If the image as several channels, only the currently active one will be used.
+
+
+### Starting the plugin
+
+From Fiji:
+
+- Open the image that you want to process.
+- Launch the plugin: `Plugins>Annotation>nnInteractive`
+- Wait for the initialization of the plugin and the network. It will install if necessary a new python environment, activates it and then initialize nnInteractive on your image.
+- When it is ready, an interface will appear to let you select some options and a new image `Composite` will apear, with your image as first chanel, and the resulting segmentations will be added to the second chanel.
+
+### Annotate object(s)
+Once the plugin is initialized, you can quickly annotate/segment object(s) in 3D by placing prompts (some cues to indicate the object of interest) then letting nnInteractive defines the precise contour in 3D.
+
+Two modes are possible in this plugin: either you want to segment only one object, and place several prompts for the same object to define it better, or you want to select several objects at once.
+
+- Choose:
+  - `One ROI by object`: to do multiple objects at the same time by placing only one prompt (ROI) by object.
+  - `All ROIs for one object`: to do only object at a time with as many prompts (ROIs) as you want for a finer segmentation. Prompts can be positive (object is here) or negative (no object here).
+ 
+- Draw prompts and add them to the RoiManager: press `1` to add positive prompts, `2` to add negative prompts. 
+
+#### Prompts
+
+See [nnInteractive](https://github.com/MIC-DKFZ/nnInteractive) for what prompts are possible and their usage.
+
+In this Fiji plugin, currently possible options to annotate are (other ROIs might be added later, you can also file an issue to ask for one to be added):
+* Rectangle ROI -> nnInteractive bounding boxes
+* Point ROI -> nnInteractive point seed
+* Line ROI -> nnInteractive scribble. In the Fiji side, it can be any type of line ROI (single line, segmented line, or freehand line).
+
+![Possible ROI to use](./media/nninterappose/RoiToolbar.png)
+
+If you want the prompt to be a positive interaction (see nnInteractive documentation), press `1` to add the current ROI to the ROIManager as a positive one. 
+For a negative prompt (relevant in `All ROIs for one object` mode), press `2` to add the current selection to the RoiManager as a negative one.
+
+
+### Segment
+When you have added all the prompts for this iteration, click the button `Segment from ROIs`, or press `0` and wait for the process to finish.
+
+The new label(s) will be added in the second chanel of the Composite image.
+
+By default, all the prompts (ROIs) that you placed are removed after the computation, so that you can start another iteration (segmentation another object).
+However, when segmenting complex objects, it might be necessary to add iteratively prompts, try to segment, remove the result and add prompts to improve it.
+For this, select the option `keep ROIs` so that the prompts will not be removed. 
+You can still remove them manually in the ROIManager afterwards.
+
+## Issue
+
+If you encountered a problem using the plugin, or to ask for a new feature, please fill an issue on the [github repository](https://github.com/Image-Analysis-Hub/nnInterappose/issues).Please give as many details as possible.
+
+You can also post a new question on the [imagesc forum](https://forum.image.sc/), mentionning that the question is related to nnInterappose plugin.
+
+To delete a segmented object when the segmentation is not satisfaisante, press `Control` and `left-click on the object.
+
+