DeepD3 inference

Open the inference mode using deepd3-inference. Load your stack of choice (we currently support TIF stacks) and specify the XY and Z dimensions. Next, you can segment dendrites and dendritic spines using a DeepD3 model from the Model Zoo by clicking on Analyze -> Segment dendrite and spines. Afterwards, you may clean the predictions by clicking on Analyze -> Cleaning. Finally, you may build 2D or 3D ROIs using the respective functions in Analyze. To test the 3D ROI building, double click in the stack to a region of interest. A window opens that allows you to play with the hyperparameters and segments 3D ROIs in real-time.

All results can be exported to various file formats. For convenience, DeepD3 saves related data in its “proprietary” hdf5 file (that you can open using any hdf5 viewer/program/library). In particular, you may export the predictions as TIF files, the ROIs to ImageJ file format or a folder, the ROI map to a TIF file, or the ROI centroids to a file.

Most functions can be assessed using a batch command script located in deepd3/inference/batch.py.