5 in 2025: our top methods papers of the year

As summer draws to a close and the academic year picks up again, we wanted to take this opportunity to highlight five exciting lab methods published in 2025, covering cell culture, AI, spectroscopy, microscopy and CRISPR. From analyzing molecules on the atomic level to rapidly harvesting organoids with a gentle solution, researchers have unveiled updates to technologies and techniques that are furthering life science research. A cell culture update: an enzyme-free alcohol-based organoid harvesting solution In need of a rapid, high-yield method for harvesting organoids and patient-derived organoids from common scaffold matrices? Solution for Harvesting Organoids Efficiently, SHOE, could be your answer. In this article, Maillard et al. report on the development of an enzyme-free organoid harvesting solution designed to address key limitations of existing methods. Their alcohol-based approach enables high cell recovery at room temperature in under five minutes, offering a rapid and gentle alternative to commercial solutions [1]. As the use of 3D cell culture continues to grow, with researchers looking to produce complex 3D models to investigate biological processes, this approach is one to watch in 3D cell culture methods. RNA extraction and RNA-sequencing method for transcriptomic analysis of Mycobacterium tuberculosis This article proposes a complete wet-lab and computational protocol for RNA-sequencing of Mycobacterium tuberculosis including RNA extraction, rRNA depletion, cDNA library preparation, high-throughput sequencing, and differential expression analysis. An AI update: ChatGPT data analyst and its implications for evaluating spheroids Everyone is talking about the power of AI, and its application in life sciences is no exception. From drug discovery and development to genomics and diagnostics, AI is reshaping the life sciences by offering an alternative to traditional methods. With the goal of improving efficiency and standardization in spheroid quality, this article by Sakamoto et al. leverages the power of AI to evaluate the shape and size of adipose-derived stem-cell spheroids [2]. The researchers’ approach offers advantages over traditional manual methods, which are often time-consuming and labor-intensive, by reducing bias and improving reproducibility. Given how crucial spheroid size and shape are for the quality control of cell-based products, the use of AI for analysis offers an efficient solution for screening microscopic images, opening new possibilities, particularly in regenerative medicine and tissue engineering. A spectroscopy update: analyzing molecules on the atomic level Powered by the same technology as MRI, nuclear magnetic resonance (NMR) spectroscopy is used to analyze molecular structures; however, its resolution isn’t high enough to sense individual atoms. Researchers at Purdue University (IN, USA) sought to remedy this limitation. They created imperfections called spin defects in ultrathin hexagonal boron nitride – a 2D material – by embedding the carbon 13 isotope. They found that when a biological molecule was placed on top of the 2D material, it influenced the spin defects embedded in the material, informing the signal registered with magnetic resonance and providing atomic-level information about the structure of the molecule [3]. “This is the first time people used carbon 13 to create a spin defect in hexagonal boron nitride,” commented senior author Tongcang Li. “Our work advances the understanding of spin defects in hexagonal boron nitride and provides a pathway to enhance quantum sensing with nuclear spins as quantum memories.” A novel device for buffy coat collection The authors developed a 3D-printed device with eight radial channels designed for precise aspiration of the buffy coat layer from centrifuged whole blood. The device interfaces with standard laboratory equipment and facilitates collection of enriched cell populations with minimal red cell contamination. A microscopy update: enhancing 3D super-resolution microscopy Three-dimensional structured illumination microscopy (3DSIM) is a valuable super-resolution imaging tool, revealing fine details within cells. It relies on uniform and stable illumination patterns, which can be disrupted by optical aberrations, sample-induced distortions or fluctuating fluorescence signals. To overcome these disruptions, researchers at Nanjing University of Science and Technology (China) have recently extended a computational enhancement, which has been successfully applied to 2D structured illumination microscopy, to improve stability and clarity of 3DSIM, called principal component analysis (PCA). PCA is a reconstruction framework that can compensate for spatial nonuniformities of illumination parameters by cutting through the chaos of distorted signals to the underlying data. When applied in the lab, it outperformed standard reconstruction pipelines, allowing researchers to get even more from their 3DSIM studies [4]. A CRISPR update: Cas12a for simultaneous multiplexed gene editing CRISPR–Cas9 has long been established as the gene-editing technology that can target, delete, replace or modify single gene sequences using a single guide RNA; however, its ability to edit multiple gene sequences simultaneously has historically been limited. Back in March, Yale University (CT, USA) researchers developed a CRISPR tool with multiplex capabilities, allowing for the simultaneous assessment of multiple genetic alterations. This new tool is called CRISPR-Cas12a, which the researchers expressed in four mouse lines to assess the impact of multiple genetic changes involved in a variety of immune system responses. The Cas12a mice showed no Cas12a-related pathology while enabling the researchers to efficiently engineer their genomes at multiple sites simultaneously [5]. 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