Key concepts
The ideas behind Cytely - a cloud-native platform that treats microscopy data like flow cytometry so you can explore populations without losing single-cell context.
Data-driven microscopy
Traditional microscopy analysis is a linear, manual bottleneck - acquiring data, shuffling files across hard drives, and running fragile scripts or manual counts. Cytely replaces that with a unified cloud environment that links quantitative metrics (scatter plots, gates) directly to visual evidence (cell images), so you can explore whole populations while still inspecting single cells instantly.
Acquisition & ingestion
Every experiment starts by ingesting images into Cytely's secure cloud. You can drag and drop existing files from the dashboard - see the Quickstart for the full upload flow - or stream data directly from a microscope with Cytely Bridge. Either way, Cytely preserves acquisition metadata and creates a single lab context - a digital twin of the experiment ready for analysis.
Cytely Bridge
Cytely Bridge is middleware that connects your microscope's software to the Cytely Cloud. As the microscope scans, images stream to the cloud with standardised parameters and full metadata. During analysis you can also click Trigger acquisition to instruct the microscope to re-image objects of interest at higher resolution.
Bridge currently supports Nikon NIS-Elements via the JOBS module, with Zeiss support in alpha.
Workflow Builder
The Workflow Builder is a visual, no-code environment for defining how Cytely identifies cells and objects. Instead of a black-box analysis, you build a transparent, reproducible pipeline by connecting nodes - for example a Gaussian filter to reduce noise, a background segmentation, a watershed to separate touching cells, a size filter to drop debris, and finally an object measurement node that extracts area, circularity, and intensity for every detected object. Running the workflow processes the whole dataset in parallel in the cloud.
Ready-to-go assays & Replicate
Cytely ships a library of pre-validated assays (for example a standard phagocytosis assay or a HeLa transfection efficiency workflow). You can also Replicate any existing workflow, tweak parameters for your sample, and save the result as a new custom assay - turning analyses into reusable, shareable building blocks.
Data Explorer
The Data Explorer is where Cytely's cytometric approach shows up. Scatter plots sit at the top, a gallery of cropped cell images sits bottom-left, and the full overview map sits bottom-right. Draw a gate on a plot and the gallery and map instantly filter to just the cells inside it, so an outlier on a graph is one click away from the actual cell in the sample.
Plots are not created automatically. You add each scatter plot, histogram, bar chart, or table yourself in the Data Explorer and choose the measurements it uses.
Sharing & replicating
A Cytely share link opens a full interactive Data Explorer for collaborators - they can inspect your gates and click through plots. Changes a recipient makes to the shared view are not saved back to your dataset, and the link does not give access to other experiments in your account. Because the analysis workflow travels with the dataset, a reviewer can also re-run your exact pipeline, or Replicate it against their own data, making reproducibility the default rather than an afterthought.
An account can also hold a team with more than one user. Team members can open each other's datasets, adjust each other's workflows, and add or remove plots and gates in the Data Explorer.