Method for generating a series of ultra-thin sections using an ultramicrotome, method for three-dimensional reconstruction of a microscopic sample, ultramicrotome system and computer program

A system for three-dimensional reconstruction of a microscopic sample, the system comprising:

• an ultramicrotome system for generating a series of ultra-thin sections of a microscopic sample, the ultramicrotome system being configured to detach the series of ultra-thin sections from the sample, to cause the series of sections to float on a liquid surface of a water bath, and to thereafter collect and transfer the series of sections onto a solid carrier element, wherein the series of sections are being stretched caused by the floating to counteract deformations caused by the detaching, the ultramicrotome system comprising:
• a monitoring system comprising a camera, the monitoring system being configured to:
• determine for at least one of the each respective section of a plurality of consecutive sections detached from the sample, a position and an orientation on the solid carrier element by:
• acquiring moving-image data using the camera as the plurality of consecutive sections are being transferred onto the solid carrier element, and
• monitoring placements of the plurality of consecutive sections onto the solid carrier element by tracking the plurality of consecutive sections in the moving-image data, so that the plurality of consecutive sections is associated with a sequence in which the plurality of sections is detached from the microscopic sample and hence with positions in the microscopic sample;
• and
• obtain monitoring data, wherein the monitoring data comprise or are used in generating a dataset comprising, for at least one of the sections detached from the sample for which the position and the orientation on the solid carrier element is determined, a position indicator and an orientation indicator relative to a reference position or orientation;
• and
• a microscopic device and an image analysis system comprising one or more processors configured to:
• microscopically investigate the series of sections of the microscopic sample, and
• acquire section image data, wherein the section image data is assembled into a volume image, and wherein the assembling the section image data into the volume image is performed based on the monitoring data obtained using the monitoring system or based on data derived from the monitoring data.