Spatial components of molecular tissue biology

G Palla, DS Fischer, A Regev, FJ Theis - Nature Biotechnology, 2022 - nature.com
Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly
evolving, making it possible to comprehensively characterize cells and tissues in health and …

Spatial omics and multiplexed imaging to explore cancer biology

SM Lewis, ML Asselin-Labat, Q Nguyen, J Berthelet… - Nature …, 2021 - nature.com
Understanding intratumoral heterogeneity—the molecular variation among cells within a
tumor—promises to address outstanding questions in cancer biology and improve the …

Cellpose 2.0: how to train your own model

M Pachitariu, C Stringer - Nature methods, 2022 - nature.com
Pretrained neural network models for biological segmentation can provide good out-of-the-
box results for many image types. However, such models do not allow users to adapt the …

TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines

D Ershov, MS Phan, JW Pylvänäinen, SU Rigaud… - Nature …, 2022 - nature.com
TrackMate is an automated tracking software used to analyze bioimages and is distributed
as a Fiji plugin. Here, we introduce a new version of TrackMate. TrackMate 7 is built to …

Specialized astrocytes mediate glutamatergic gliotransmission in the CNS

R de Ceglia, A Ledonne, DG Litvin, BL Lind, G Carriero… - Nature, 2023 - nature.com
Multimodal astrocyte–neuron communications govern brain circuitry assembly and function.
For example, through rapid glutamate release, astrocytes can control excitability, plasticity …

Functional partitioning of transcriptional regulators by patterned charge blocks

H Lyons, RT Veettil, P Pradhan, C Fornero… - Cell, 2023 - cell.com
Components of transcriptional machinery are selectively partitioned into specific
condensates, often mediated by protein disorder, yet we know little about how this specificity …

CellProfiler 4: improvements in speed, utility and usability

DR Stirling, MJ Swain-Bowden, AM Lucas… - BMC …, 2021 - Springer
Background Imaging data contains a substantial amount of information which can be difficult
to evaluate by eye. With the expansion of high throughput microscopy methodologies …

Multimodal data integration using machine learning improves risk stratification of high-grade serous ovarian cancer

KM Boehm, EA Aherne, L Ellenson, I Nikolovski… - Nature cancer, 2022 - nature.com
Patients with high-grade serous ovarian cancer suffer poor prognosis and variable response
to treatment. Known prognostic factors for this disease include homologous recombination …

Tissue-resident macrophages provide a pro-tumorigenic niche to early NSCLC cells

M Casanova-Acebes, E Dalla, AM Leader, J LeBerichel… - Nature, 2021 - nature.com
Macrophages have a key role in sha** the tumour microenvironment (TME), tumour
immunity and response to immunotherapy, which makes them an important target for cancer …

Light sheet fluorescence microscopy

EHK Stelzer, F Strobl, BJ Chang, F Preusser… - Nature Reviews …, 2021 - nature.com
Light sheet fluorescence microscopy (LSFM) uses a thin sheet of light to excite only
fluorophores within the focal volume. Light sheet microscopes (LSMs) have a true optical …