The MaskRCNN ZeroCostDL4Mic notebook is currently in beta. To enable bioimaging tasks, the notebook is designed to take .csvs as annotation files which can be created and exported from the ROI manager in Fiji/ImageJ. You can use our Fiji macro (see link below) to export annotations from Fiji's ROI manager into a format that is accepted by the notebook.

To annotate data for the MaskRCNN notebook using the macro, follow the steps below.

1. Open our Annotate_MRCNN_Data macro for Fiji, download here.
2. Open the images you wish to annotate in Fiji.
3. Use the Polygon selection tool to outline the objects you wish to segment and add each object to the ROI manager using CTRL + t.
4. Once all the objects are labelled, click on an ROI in the ROI manager and click 'rename'.
5. Enter the class name of the object you annotated and repeat this for each object on the image.
6. When all objects are annotated, enter the directory you want to save the annotations to, into the first line of the macro.
7. Click Run on the macro. This will save the annotations as a csv file in the directory chosen in 5, and will close the image.
8. Repeat this for all the images you want to annotate.

To find out more about MaskRCNN, also have a look at the original repository: https://github.com/matterport/Mask_RCNN which contains many questions and answers about MaskRCNN. We will also add some tips and tricks for the use of the ZeroCostDL4Mic notebook here soon.