CeNDeR-annotation

This toolkit can view and annotate whole brain imaging data.

Human annotation and proofreading toolkit

Human annotation contains two main procedures:

1. Division, convert raw tiff images into 3D image stacks

   image_stack=import_micromanager_data_and_reshape;

   Read and divide tiff data according to your 3D imaging setup. The output should be a num_of_volumes × 1 cell. Each element of the cell is a volume, represented by a height × width × num_of_slices uint16 matrix.

2. Annotation, draw and label bounding boxes manually; or proofread the inferred bounding boxes. This part runs in MATLAB.

   • If you don't have bounding boxes :

     whole_brain_imaging(image_stack)

     Show the image stack. To draw a bounding box by hand, select Annotation->Bound neuron in the menu bar, and then left-click to draw a rectangle in the GUI. To label a bounding box, select Annotation->Assign index to outlier box and left-click inside the bounding box.

   • If you have bounding boxes and want to proofread them:

     whole_brain_imaging(image_stack, neuron_box)

     To correct the ID of a bounding box, select Annotation->Assign index to outlier box and then left-click inside the bounding box.

   Select File->Export to save the bounding boxes to workspace and hard disk.