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
.