Auto Annotator

The RedBrick AI Auto Annotator is an automated segmentation tool that allows teams to easily generate segmentation masks for hundreds of different structures on CT and MR images, which are then inserted into a Project pipeline as pre-labels.

To use Auto Annotator, you must have an active Boost instance available in your Organization.

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Adding Auto Annotator to a Project

The decision to utilize Auto Annotator for a Project must be made at Project creation.

After a Project has been created, there is no way to retroactively add Auto Annotator to it, as the model will be added to the Project pipeline as a pre-Stage.

If you have an active Boost instance in your Organization, you will notice that Step (4) of standard Project creation looks slightly different:

1. The Auto Annotator toggle;
2. Object Label mapping window;
3. Model URL selection dropdown;

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Mapping Object Labels

After you’ve enabled Auto Annotator in a Project, you must map the labels that the algorithm will generate to a corresponding entry in your Redbrick Taxonomy.

Click on Map object labels to open the Mapping window.

The Mapping Window allows you to:

1. Choose which Auto Annotator sub-type you would like to use for this specific Project;
2. Map the output of the designated model sub-type to the Object Labels of your Project’s Taxonomy;

Each entry in the Auto Annotator Labels list can only be mapped once. However, Taxonomy Labels can be mapped to as many structures as you’d like.

Consider the example below, where the model output for kidney_right and kidney_left are both mapped to a single RedBrick Object Label called Kidney.

Once you have finished mapping your labels, click on Save changes.

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Selecting a Model

If you have multiple models integrated with RedBrick AI, you can use the dropdown field to select which model should run on this specific Project.

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Running Auto Annotator in a Project

Once your Project is created, any data that you upload or integrate to the Project will automatically pass through the Auto Annotator pre-Stage, where automated annotation will occur.

There is nothing that the user needs to do for Tasks in the Auto Annotator pre-Stage. After the Auto Annotator is done generating labels, the Task will automatically move to the next Stage in your Project pipeline.

Once the Tasks have reached the next Stage in your pipeline, your team can begin work on it.

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Boost Models

When creating a Project with Auto Annotator enabled, you have the opportunity to select a wide range of potential segmentations for your pre-Stage. A comprehensive list of all libraries and structures can be found below.

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total

spleen kidney_right kidney_left gallbladder liver stomach pancreas adrenal_gland_right adrenal_gland_left lung_upper_lobe_left lung_lower_lobe_left lung_upper_lobe_right lung_middle_lobe_right lung_lower_lobe_right esophagus trachea thyroid_gland small_bowel duodenum colon urinary_bladder prostate kidney_cyst_left kidney_cyst_right sacrum vertebrae_S1 vertebrae_L5 vertebrae_L4 vertebrae_L3 vertebrae_L2 vertebrae_L1 vertebrae_T12 vertebrae_T11 vertebrae_T10 vertebrae_T9 vertebrae_T8 vertebrae_T7 vertebrae_T6 vertebrae_T5 vertebrae_T4 vertebrae_T3 vertebrae_T2 vertebrae_T1 vertebrae_C7 vertebrae_C6 vertebrae_C5 vertebrae_C4 vertebrae_C3 vertebrae_C2 vertebrae_C1 heart aorta pulmonary_vein brachiocephalic_trunk subclavian_artery_right subclavian_artery_left common_carotid_artery_right common_carotid_artery_left brachiocephalic_vein_left brachiocephalic_vein_right atrial_appendage_left superior_vena_cava inferior_vena_cava portal_vein_and_splenic_vein iliac_artery_left iliac_artery_right iliac_vena_left iliac_vena_right humerus_left humerus_right scapula_left scapula_right clavicula_left clavicula_right femur_left femur_right hip_left hip_right spinal_cord gluteus_maximus_left gluteus_maximus_right gluteus_medius_left gluteus_medius_right gluteus_minimus_left gluteus_minimus_right autochthon_left autochthon_right iliopsoas_left iliopsoas_right brain skull rib_left_1 rib_left_2 rib_left_3 rib_left_4 rib_left_5 rib_left_6 rib_left_7 rib_left_8 rib_left_9 rib_left_10 rib_left_11 rib_left_12 rib_right_1 rib_right_2 rib_right_3 rib_right_4 rib_right_5 rib_right_6 rib_right_7 rib_right_8 rib_right_9 rib_right_10 rib_right_11 rib_right_12 sternum costal_cartilages

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total_MR

spleen kidney_right kidney_left gallbladder liver stomach pancreas adrenal_gland_right adrenal_gland_left lung_left lung_right esophagus small_bowel duodenum colon urinary_bladder prostate sacrum vertebrae intervertebral_discs spinal_cord heart aorta inferior_vena_cava portal_vein_and_splenic_vein iliac_artery_left iliac_artery_right iliac_vena_left iliac_vena_right humerus_left humerus_right scapula_left scapula_right clavicula_left clavicula_right femur_left femur_right hip_left hip_right gluteus_maximus_left gluteus_maximus_right gluteus_medius_left gluteus_medius_right gluteus_minimus_left gluteus_minimus_right autochthon_left autochthon_right iliopsoas_left iliopsoas_right brain

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lung_vessels

lung_vessels (cite paper) lung_trachea_bronchia

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body

body body_trunc body_extremities skin

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body_mr

body_trunc body_extremities (for MR images)

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vertebrae_mr

sacrum vertebrae_L5 vertebrae_L4 vertebrae_L3 vertebrae_L2 vertebrae_L1 vertebrae_T12 vertebrae_T11 vertebrae_T10 vertebrae_T9 vertebrae_T8 vertebrae_T7 vertebrae_T6 vertebrae_T5 vertebrae_T4 vertebrae_T3 vertebrae_T2 vertebrae_T1 vertebrae_C7 vertebrae_C6 vertebrae_C5 vertebrae_C4 vertebrae_C3 vertebrae_C2 vertebrae_C1

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cerebral_bleed

intracerebral_hemorrhage (cite paper)

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hip_implant

hip_implant

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pleural_pericard_effusion

pleural_effusion (cite paper) pericardial_effusion (cite paper)

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head_glands_cavities

eye_left eye_right eye_lens_left eye_lens_right optic_nerve_left optic_nerve_right parotid_gland_left parotid_gland_right submandibular_gland_right submandibular_gland_left nasopharynx, oropharynx hypopharynx nasal_cavity_right nasal_cavity_left auditory_canal_right auditory_canal_left soft_palate hard_palate (cite paper)

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head_muscles

masseter_right masseter_left temporalis_right temporalis_left lateral_pterygoid_right lateral_pterygoid_left medial_pterygoid_right medial_pterygoid_left tongue digastric_right digastric_left

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headneck_bones_vessels

larynx_air thyroid_cartilage hyoid cricoid_cartilage zygomatic_arch_right zygomatic_arch_left styloid_process_right styloid_process_left internal_carotid_artery_right internal_carotid_artery_left internal_jugular_vein_right internal_jugular_vein_left (cite paper)

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headneck_muscles

sternocleidomastoid_right sternocleidomastoid_left superior_pharyngeal_constrictor middle_pharyngeal_constrictor inferior_pharyngeal_constrictor trapezius_right trapezius_left platysma_right platysma_left levator_scapulae_right levator_scapulae_left anterior_scalene_right anterior_scalene_left middle_scalene_right middle_scalene_left posterior_scalene_right posterior_scalene_left sterno_thyroid_right sterno_thyroid_left thyrohyoid_right thyrohyoid_left prevertebral_right prevertebral_left (cite paper)

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liver_vessels

liver_vessels liver_tumor (cite paper)

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oculomotor_muscles:

skull eyeball_right lateral_rectus_muscle_right superior_oblique_muscle_right levator_palpebrae_superioris_right superior_rectus_muscle_right medial_rectus_muscle_left inferior_oblique_muscle_right inferior_rectus_muscle_right optic_nerve_left eyeball_left lateral_rectus_muscle_left superior_oblique_muscle_left levator_palpebrae_superioris_left superior_rectus_muscle_left medial_rectus_muscle_right inferior_oblique_muscle_left inferior_rectus_muscle_left optic_nerve_right

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lung_nodules

lung lung_nodules (provided by BLUEMIND AI: Fitzjalen R., Aladin M., Nanyan G.) (trained on 1353 subjects, partly from LIDC-IDRI)

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kidney_cysts

kidney_cyst_left, kidney_cyst_right (strongly improved accuracy compared to kidney_cysts inside of total task)

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breasts

breast