Abstract: Provided in some aspects are methods for light-controlled in situ surface patterning of a substrate comprising a step of blocking or ablating oligonucleotide molecules in a boundary region separating a plurality of spot regions, and attaching oligonucleotides to oligonucleotide molecules in a first one or more of the spot regions.

Abstract: The present disclosure relates in some aspects to methods and compositions for manufacturing molecular arrays using a hybrid approach comprising using non-contact printing (e.g., using inkjet printing, slot die coating, and/or blade coating) and photolithography-guided oligonucleotide hybridization and ligation. In particular, the molecular arrays can be used for determining spatial patterns of abundance and/or expression of a biological target in a sample.

Abstract: Provided in some aspects are methods for light-controlled in situ surface patterning of a substrate. Compositions such as nucleic acid arrays produced by the methods are also disclosed. In some embodiments, a method disclosed herein comprises using photoresist for photocontrollable hybridization and/or ligation of nucleic acid molecules, wherein photoresist removal allows hybridization and/or ligation of nucleic acid molecules at the exposed area. A large diversity of barcodes can be created in molecules on the substrate via sequential rounds of light exposure, hybridization, and ligation.

Abstract: The present disclosure is directed to a method for designing an aperture in a mask for inspecting a wafer. The method includes the steps of scanning a collection plane of the wafer at a plurality of points and collecting data for at least a part of the wafer. The method also includes the step of mapping the data. A further step of the method includes configuring the aperture based on the mapped data.

Abstract: An inspection system with selectable apodization includes a selectably configurable apodization device disposed along an optical pathway of an optical system. The apodization device includes one or more apodization elements operatively coupled to one or more actuation stages. The one or more actuation stages are configured to selectably actuate the one or more apodization elements along one or more directions. The inspection system includes a control system communicatively coupled to the one or more actuation stages. The control system is configured to selectably control an actuation state of at the one or more apodization elements so as to apply a selected apodization profile formed with the one or more apodization elements.

Abstract: An inspection system with selectable apodization includes a selectably configurable apodization device disposed along an optical pathway of an optical system. The apodization device includes one or more apodization elements operatively coupled to one or more actuation stages. The one or more actuation stages are configured to selectably actuate the one or more apodization elements along one or more directions. The inspection system includes a control system communicatively coupled to the one or more actuation stages. The control system is configured to selectably control an actuation state of at the one or more apodization elements so as to apply a selected apodization profile formed with the one or more apodization elements.

Abstract: An inspection system with selectable apodization includes an illumination source configured to illuminate a surface of a sample, a detector configured to detect at least a portion of light emanating from the surface of the sample, the illumination source and the detector being optically coupled via an optical pathway of an optical system, a selectably configurable apodization device disposed along the optical pathway, wherein the apodization device includes one or more apodization elements operatively coupled to one or more actuation stages configured to selectably actuate the one or more apodization elements along one or more directions, and a control system communicatively coupled to the one or more actuation and configured to selectably control apodization of illumination transmitted along the optical pathway by controlling an actuation state of the one or more apodization elements.

Abstract: Disclosed are mechanisms for selectively filtering spatial portions of light emanating from a sample under inspection within an optical system. In one embodiment, a programmable spatial filter (PSF) is constructed from materials that are compatible with light in a portion of the UV wavelength range. In a specific implementation, the PSF is constructed from a UV compatible material, such as a polymer stabilized liquid crystal material. In a further aspect, the PSF also includes a pair of plates that are formed from a UV grade glass. The PSF may also include a relatively thin first and second ITO layer that results in a sheet resistance between about 100 and about 300 &OHgr; per square.