Various methods and devices for spatial molecular analysis from tissue is provided. For example, a method of spatially mapping a tissue sample is provided with a microarray having a plurality of wells, wherein adjacent wells are separated by a shearing surface; overlaying said microarray with a tissue sample; applying a deformable substrate to an upper surface of said tissue sample; applying a force to the deformable substrate, thereby forcing underlying tissue sample into the plurality of wells; shearing the tissue sample along the shearing surface into a plurality of tissue sample islands, with each unique tissue sample island positioned in a unique well; and imaging or quantifying said plurality of tissue sample islands, thereby generating a spatial map of said tissue sample. The imaging and/or quantifying may use a nucleic acid amplification technique.

The invention relates to a printing control device (10) to control printing of a cover layer on a tissue or cell sample to be examined, a system (1) for printing of a cover layer (1) on a tissue or cell sample to be examined, a method to control printing of a cover layer on a tissue or cell sample to be sample to be examined, a computer program element for controlling such device or system for performing such method and a computer readable medium having stored such computer program element. The printing control device (10) comprises an imaging unit (11) and a printing control unit (12). The imaging unit (11) is configured to provide image data of the sample, and to determine a local image parameter from the image data. The local image parameter relates to local tissue porosity and/or a local capillary force of the sample. The printing control unit (12) is configured to control a printing parameter for printing the cover layer on the sample based on the local image parameter.

A trace evidence material (TEM) collection device is disclosed that enables crime scene investigators to quickly and easily collect, analyze, annotate, securely store and electronically distribute images of large amounts of trace evidence materials and related crime scene information while also helping to comply with required trace evidence recovery procedures and documentation requirements. The TEM collection device includes a reusable handle and cassette drive mechanism, which may be used with a plurality of single-use cassettes. Each cassette includes a TEM collection media (such as a collection tape or swabbing pads attached to a substrate) that when moved across a surface is capable of collecting TEMs located on the surface. Preferably, each cassette also includes a sealing assembly that seals the TEM collection media after collection of the TEMs so as to preserve the collected TEMs.

The present application relates generally to image tiling, including but not limited to systems and methods of fast whole slide tissue tiling. A computing system may identify a first image of a first dimension from which to select one or more tiles. The computing system may perform a reduction operation on the first image to generate a second image of a second dimension. The computing system may apply a thresholding operation on the second image to identify a first set of pixels corresponding to the presence of the feature and a second set of pixels corresponding to the absence of the feature based on an intensity of each pixel in the second image. The computing system may select, from a plurality of tiles corresponding to the first image, a subset of tiles corresponding to the first set of pixels identified from the second image.

A method of electron microscopy imaging of samples, using an electron microscope (100) having a microscope column (10) and a transfer device (11) with a grid carriage (12), comprises the steps of preparing multiple samples (1) on a single electron microscopy grid (2), including dispensing the samples (1) with a dispenser device (30) on distinct positions on the grid (2), introducing the grid (1) with the transfer device (11) into the microscope column (10), and electron microscopy imaging of the samples (1), wherein the preparing step includes holding the grid (2) on the grid carriage (12) of the transfer device (11) or on a grid holder device (20) provided at the electron microscope (100) and dispensing the samples (1) on the grid (2) while holding it on the grid carriage (12) or on the grid holder device (20). Furthermore, an electron microscope (100) for electron microscopy imaging of samples is described.

In an example, a method includes producing a set of projected sample characterization values associated with each of a plurality of processing axes and identifying a preferred processing axis based on the projected sample characterization values. In another representative example, a method includes extracting a sample specimen, producing a sample image of the sample specimen, identifying a preferred sample tilt angle, and rotating the sample specimen to an orientation corresponding to a preferred sample tilt angle. The method further includes processing the sample specimen to produce a lamella. In another representative example, a system includes a focused ion beam (FIB) system, a sample holder, a stage, and a controller operable to cause the stage to rotate the sample specimen relative to the ion beam axis such that the ion beam approaches the sample specimen along a preferred processing axis.

Disclosed is a method for capturing the spatial molecular profiling of a biological mass formed from biological material, comprising the steps of: a) providing a transected biological mass, for example a tumour, the transection exposing at least a portion of the mass; b) providing a solid support of an area at least equalling the area of said portion of the mass; c) transferring biological material from the portion of the mass to the support to provide on the support a two dimensional imprint of the biological material present at the portion of the mass; and d) performing a biological assay of the transferred biological material from different predetermined locations of the imprint in order to determine the spatial molecular profile of the portion of the mass.

In accordance with preferred embodiments of the present invention, a method for imaging tissue, for example, includes the steps of mounting the tissue on a computer controlled stage of a microscope, determining volumetric imaging parameters, directing at least two photons into a region of interest, scanning the region of interest across a portion of the tissue, imaging a plurality of layers of the tissue in a plurality of volumes of the tissue in the region of interest, sectioning the portion of the tissue and imaging a second plurality of layers of the tissue in a second plurality of volumes of the tissue in the region of interest, detecting a fluorescence image of the tissue due to said excitation light; and processing three-dimensional data that is collected to create a three-dimensional image of the region of interest.

An improved process workflow and apparatus for S/TEM sample preparation and analysis is provided. Preferred embodiments provide improved methods for an automated recipe TEM sample creation, especially for small geometry TEM lamellae, employing CAD data to automatically align various stages of sample preparation. The process automatically verifies and aligns the position of FIB-created fiducials by masking off portions of acquired images, and then comparing them to synthesized images from CAD data. SEM beam positions are verified by comparison to images synthesized from CAD data. FIB beam position is also verified by comparison to already-aligned SEM images, or by synthesizing an FIB image from CAD using techniques for simulating FIB images. The automatic alignment techniques herein allow creation of sample lamellas at specified locations without operator intervention.

The present application relates generally to image tiling, including but not limited to systems and methods of fast whole slide tissue tiling. A computing system may identify a first dimension of a first image from which to select one or more tiles. The computing system may perform a reduction operation on the first image to generate a second dimension of a second image. The computing system may perform a smoothening operation on the second image. The computer system may identify a first set of pixels in the second image corresponding to a presence of a feature and a second set of pixels corresponding to an absence of the feature. The computing system may select, from a plurality of tiles corresponding to the first image, a subset of tiles corresponding to the first set of pixels identified from the second image.