Abstract: Methods and software assisting a user in working with images of histological sections to increase the user's productivity and decrease the need for extensive expertise in anatomy. In some embodiments, the methods include methods of assisting a user in creating a 3D volume image of a tissue block from a series of images of histological sections taken from the tissue block. In some embodiments, the methods include methods of automatedly registering a live-view or stored histological section image to a tissue block atlas. In some embodiments, the methods include methods of annotating a histological section image with information from a tissue block atlas based on user input(s) associated with the tissue block atlas. In some embodiments, the methods include methods of automatedly controlling operation of an imaging modality, such as an optical microscope, based on user input(s) associated with a tissue block atlas. These and other methods may be embodied in various configurations of software.

Abstract: Methods and systems for tracking one or more worms or worm-like organisms over a sequence of video frames in virtual real time. The methods and systems can include a robust organism model that accounts for shape changes that occur from one frame to another, such as peristaltic progression, longitudinal deformation, lateral deformation, and bending action. Other features disclosed include: features that allow a user to correct tracking errors, such as splitting a single organism track into two tracks, joining two organism tracks into a single track, switching locations of physical features (such as heads and tails of worms), deleting undesired tracked organisms, and manually tracing organism outlines for model fitting; features that allow a user to set tracking parameters by selecting one or more organisms having desired characteristics; features for automatedly resolving interactions between/among multiple organisms; and features for handling multiple tracking hypotheses, among others.

Abstract: Methods for preparing a biological tissue specimen for examination, such as microscopic examination, that involves applying acoustic pressure wave/shock wave (APW/SW) energy to the tissue specimen. The APW/SW energy can be applied to the tissue specimen to augment any one or more steps of processing the tissue specimen. In one example, the APW/SW energy is applied to enhance histotechnological processing of the tissue specimen. Apparatuses and systems that include APW/SW generators and that are specifically configured for processing biological tissue specimens are also disclosed.

Abstract: A movable objective lens assembly that includes an infinity-corrected objective lens providing the microscope with an optical field of view. The assembly permits the imaging of a specimen under investigation over an area of the specimen much larger than the field of view of the objective lens without moving the microscope and/or a specimen stage relative to one another. The assembly includes a mirror system and the linearly movable infinity-corrected objective lens. The mirror system includes a plurality of mirrors that provide a folded optical path that allows the objective lens to be moved relative to the specimen without moving the entire microscope. The mirror system and the objective lens are pivotably mounted relative to the rest of the microscope so as to allow the objective lens to be located substantially anywhere within a circular, or circular-sectoral, viewing area.

Abstract: A movable objective lens assembly that includes an infinity-corrected objective lens providing the microscope with an optical field of view. The assembly permits the imaging of a specimen under investigation over an area of the specimen much larger than the field of view of the objective lens without moving the microscope and/or a specimen stage relative to one another. The assembly includes a mirror system and the linearly movable infinity-corrected objective lens. The mirror system includes a plurality of mirrors that provide a folded optical path that allows the objective lens to be moved relative to the specimen without moving the entire microscope. The mirror system and the objective lens are pivotably mounted relative to the rest of the microscope so as to allow the objective lens to be located substantially anywhere within a circular, or circular-sectoral, viewing area.

Abstract: A movable objective lens assembly that includes an infinity-corrected objective lens providing the microscope with an optical field of view. The assembly permits the imaging of a specimen under investigation over an area of the specimen much larger than the field of view of the objective lens without moving the microscope and/or a specimen stage relative to one another. The assembly includes a mirror system and the linearly movable infinity-corrected objective lens. The mirror system includes a plurality of mirrors that provide a folded optical path that allows the objective lens to be moved relative to the specimen without moving the entire microscope. The mirror system and the objective lens are pivotably mounted relative to the rest of the microscope so as to allow the objective lens to be located substantially anywhere within a circular, or circular-sectoral, viewing area.

Abstract: A movable objective lens assembly that includes an infinity-corrected objective lens providing the microscope with an optical field of view. The assembly permits the imaging of a specimen under investigation over an area of the specimen much larger than the field of view of the objective lens without moving the microscope and/or a specimen stage relative to one another. The assembly includes a mirror system and the linearly movable infinity-corrected objective lens. The mirror system includes a plurality of mirrors that provide a folded optical path that allows the objective lens to be moved relative to the specimen without moving the entire microscope. The mirror system and the objective lens are pivotably mounted relative to the rest of the microscope so as to allow the objective lens to be located substantially anywhere within a circular, or circular-sectoral, viewing area.