3D masking in a computed tomography image

An apparatus for imaging a specimen, the apparatus comprising:

• a housing defining an interior chamber;
• a pedestal disposed within the interior chamber of the housing, wherein the pedestal is configured to rotate about an axis and removably couple to a container holding the specimen, wherein at least one of the pedestal and the container comprise a key;
• an x-ray imaging source disposed within the housing, the x-ray imaging source configured to project an x-ray beam inside the interior chamber and positioned a known imaging distance from the axis of the pedestal;
• a display;
• a processor;
• memory storing instructions that, when executed by the processor, cause the apparatus to perform a set of operations comprising:
• upon receiving the container holding the specimen on the pedestal, identifying a geometry of the container;
• determining a mask corresponding to the container, based on the identification of the geometry of the container;
• rotating the container and the specimen about the axis through a plurality of imaging angles;
• while rotating the container and the specimen through the plurality of imaging angles, x-ray imaging the container and the specimen with the x-ray imaging source to obtain a set of 2D images;
• based on the set of 2D images, generating a 3D image comprising a 3D representation of the specimen and a 3D representation of the container;
• applying the mask to the 3D image to mask the 3D representation of the container;
• and
• displaying, on the display, the 3D image comprising the 3D representation of the specimen and the masked 3D representation of the container.

A method for masking a container holding a specimen, the method comprising:

• receiving the container holding the specimen on a rotatable support surface in a container pose relative to the rotatable support surface, the rotatable support surface configured to rotate about an axis at an imaging distance from an x-ray imaging source;
• identifying the container;
• determining a mask corresponding to the container, based on the identification of the container;
• rotating the container and the specimen about the axis through a plurality of imaging angles;
• while rotating the container and the specimen through the plurality of imaging angles, x-ray imaging the container and the specimen with the x-ray imaging source to obtain a set of 2D images;
• based on the set of 2D images, generating a 3D image comprising a 3D representation of the specimen and a 3D representation of the container;
• estimating a mask pose of the mask in the 3D image, based at least in part on the known imaging distance;
• identifying a position of a marker on the container in the set of 2D images;
• based on the identified position of the marker, determining a tolerance of the mask;
• adjusting the mask pose of the mask based on the tolerance;
• applying the mask in the adjusted mask pose to the 3D image to mask the 3D representation of the container;
• and
• displaying the 3D image comprising the 3D representation of the specimen and the masked 3D representation of the container.