Multi-resolution in situ decoding

A system comprising:

• one or more processors;
• and
• a non-transitory computer readable storage medium communicatively coupled to the one or more processors and configured to store instructions that, when executed by the one or more processors, cause the one or more processors to perform a method comprising:
• receiving a series of first images of a biological sample, wherein the first images of the series of first images have a first optical resolution, and wherein the series of first images comprises a z-stack of images;
• identifying locations for a plurality of target analytes based on the series of first images;
• receiving at least one second image of the biological sample, wherein the at least one second image has a second optical resolution that is the same as the first optical resolution, the at least one second image corresponding to at least one decoding cycle of a plurality of decoding cycles used for in situ decoding of the plurality of target analytes, and wherein the at least one second image is computationally downsampled after acquisition to a lower optical resolution;
• and
• extracting feature data associated with all or a portion of the plurality of target analytes from the at least one second image based on the locations for the plurality of target analytes identified in the series of first images.

A method comprising:

• receiving a plurality of high-resolution images of a sample during at least a first cycle of fluorescent probing of the sample, wherein the plurality of high-resolution images comprises at least one z-stack of images representing a volume of the sample, wherein the plurality of high-resolution images is acquired using an image sensor, and wherein the plurality of high-resolution images comprises a first plurality of light signals representing a plurality of probes bound to a plurality of analytes within the sample;
• determining first positional information of the first plurality of light signals from the at least one high-resolution image;
• receiving at least one low-resolution image of the sample during at least a second cycle of fluorescent probing of the sample, wherein receiving the at least one low-resolution image comprises acquiring, using the image sensor, at least one additional high-resolution image during the at least a second cycle of fluorescent probing, and generating the at least one low-resolution image by downsampling the at least one additional high-resolution image;
• and
• determining a second plurality of light signals within the at least one low-resolution image based on the first positional information, wherein the second plurality of light signals comprises two or more colors.