Challenges
Challenge areas identified from January 2019 IBIN meeting:
– Computational
– Probe Development
– Super-Resolution
– 3D Bioimaging Instrumentation
– 3D Biomechanics
Each of these challenges is described in more detail below. Please use these as a guide for developing projects for IBIN funding.
Computational
– Develop mathematical models to interpret 3D imaging data and define collective behaviours
– Machine learning tools: Background noise removal and compensating for/tracking movement
– Quantitative analysis of shape changes in 3D volumes
– Unsupervised data acquisition – identification of features whilst imaging at different scales (AI); low resolution non-toxic to high resolution
– Developed software needs to be open source – use of online repositories (potentially through connection from IBIN hub website)
Probe Development
– Probes with long emission lifetimes to discriminate from background fluorescence. More excitation/emission wavelengths, improved QY/brightness, tuneable singlet/triplet coupling for improved blinking performance, low molecular weight and can be used in live cells
– Optogenetic probes (red/far-red) to trigger cell death/signalling in cell subpopulations
– New probes for STORM/PALM – especially for multi-colour imaging
– Need better lipid-specific dyes for live imaging and probes to image cell membrane curvature
– Need long-term probes for tracking/imaging over multiple days for 3D samples
– Need tension sensor probes that are not protein specific
– A centralised way to share probes and knowledge (website links to pre-prints and white papers)
Super-Resolution
– Need standardisation/QC and ground truth tools, calibration slides and standard samples
– Finding ways to make STORM/PALM data easier to acquire/analyse from 3D samples
– New approaches to correlate super-resolution, AFM and EM datasets from same sample
– 3D Super-resolution: deep tissue (adaptive optics, multiphoton, optogenetics)
– Imaging exosomes in situ: ways to identify populations and characterise surface markers in 3D
3D Bioimaging Instrumentation
– Instrumentation and methods for rapid accurate spectral unmixing from multiple z-slices within 3D samples (≥300um)
– Combine label-free and label multimodal, compatible with live cell/tissues – eg: Spectral imaging, fluorescence lifetime, bioluminescence (luciferase), Raman and Brillouin etc.
– Single-cell optogenetic targeting in 3D (precision); needs to be low photon dose
– Improving resolution in 3D systems; eg: adaptive optics, 2-photon light sheet
3D Biomechanics
– Analysing relationships between cells and forces combined with functional imaging of signalling
– Reproducibility of 3D models: Hydrogels to incorporate native proteins, Control pore size/crosslink/stiffness and physical properties.
– Imaging of short-term mechanical events and longer-term cell fates
– Ways to image tension between cells and nuclear morphology changes in dense 3D cultures/tissues
– Cytoskeleton tension sensors to uncouple fluidity and tension