Image Analysis
My workflow and tool set
Primary cultures, tissue preparation, IHC, confocal and super-resolution imaging, FIJI and IMARIS quantification — I work the full pipeline, from the cell on the bench to the figure in the paper, where the science finally becomes something you can see.
Full workflow
From bench to published figure
The parts that determine whether a measurement is trustworthy are almost never in the methods section. Each stage below shapes what the final number can and cannot mean.
Prepare the biological system
The work starts before the microscope is on. I culture primary astrocytes, neurons, fibroblasts, and BV2 microglia — maintaining the conditions that keep the biology stable and experimental outcomes interpretable. For brain tissue, I section at controlled thickness, preserve anatomical landmarks, and design the protocol around what the material will and won't survive.
Label and validate the readout
Fluorescence labeling determines what the image can show — and what it can't. I design IHC and ICC protocols around the biological question: antibody combinations chosen for colocalization, incubation conditions optimised for signal-to-noise, specificity checks run before the imaging session begins. When molecular context needs grounding, I connect it to PCR, Western blot, and protein quantification.
Fabricate microfluidic devices
Some experiments need a controlled microenvironment — defined gradients, isolated cell populations, steady flow conditions that a Petri dish cannot provide. I design and fabricate PDMS microfluidic chips from photolithography to finished device, then integrate live cell culture with the platform. It means thinking about the biology and the engineering in the same breath.
Acquire the image
Different questions require different microscopes, and the acquisition parameters are chosen for the tissue — not the protocol. I work across confocal, nonlinear two-photon, super-resolution SIM, digital holographic, and fluorescence imaging. Calcium imaging adds a temporal dimension. When the optical limit is not enough, I prepare biological samples for scanning electron and atomic force microscopy.
Analyse and interpret
The image holds the argument — but only after it has been measured. I quantify fluorescence with controlled ROI placement and background subtraction, work in 3D for volumetric data, and build batch pipelines when the dataset is too large for manual measurement. The result is not a number in isolation but an interpretation: connected back to the biological question, with acquisition context preserved so the next reader can evaluate it.