We’re excited to share our latest update to Cytely! Over the past few weeks, our team has been hard at work adding new capabilities to make your dataset exploration faster, more flexible, and easier to navigate.

Here are the three key updates you can start using today:

Lightning-Fast Performance

Cytely now runs on a brand-new analysis engine that significantly improves load times and responsiveness, even when you are working with massive single-cell datasets.

Quicker load times: Datasets open faster than ever before. Responsive visuals: Plots and graphs respond immediately to your inputs. Seamless navigation: Interactions across the entire interface feel instantaneous.

Enhanced Interactivity in the Data Explorer

We’ve completely upgraded how you interact with your data, giving you ultimate control over your workspace and making population exploration highly intuitive.

• Interactive Plots: Toggle groups directly within your plots to instantly focus on specific populations or compare subsets.
• Customizable Workspace: Plots are now fully movable, allowing you to arrange your dashboard exactly how you want it.
• Granular Statistics: Tables now dynamically display statistics for individual, selected groups.
• Easy Exports: With just a click, you can download single-cell images, export your plots, or copy table statistics straight to your clipboard.
• Redesigned 'Images' Tab: We've made browsing cells much more flexible. You can easily edit groups, sort images (by name, date, group, or detections), and update the layout of your overview map. Plus, when you select an individual cell, Cytely instantly locates it within the full image overview so you never lose spatial context.

Expanded Analysis Possibilities

To help you get more out of your quantitative measurements without leaving the platform, we’ve added several powerful new analysis capabilities directly into Cytely:

Sub-masks: Perform highly detailed measurements within segmented objects using single or multiple sub-masks. Correlation Analysis: You can now run correlation analyses using both Pearson and Manders' metrics. Ratiometric Analysis: Easily enable direct comparisons between channel intensities within individual cells.

Bonus: Direct In-App Support

Need help setting up an experiment? We’ve added a new live chat feature! Simply write us a line directly within Cytely, and our team will jump in to help you out.

All of these features are live right now.

Log in to Cytely to explore these updates with your own datasets today!

This week marks a major milestone: our brand-new processing engine is now live for all users! Designed to handle massive datasets with ease, it increases performance by more than 10x on large datasets. Alongside this speed boost, we are introducing powerful new ways to navigate your data spatially, from whole-plate overviews down to individual cell context.

What shipped this week:

New Engine: The new engine is now the standard for all accounts, ensuring that analyzing tens of thousands of objects remains a lightning-fast experience. With a flexible database under the hood we will be able to query the data in new ways.

Thumbnail to Sample Navigation: We continue adding more ways to explore your data. When investigating a specific object thumbnail, you can now navigate to that object's exact location within the full sample view, highlighting it for immediate context.

Well Plate View (Alpha): We are now in alpha with visual navigator for plate-based experiments. You can now generate heatmaps for extracted parameters (e.g., mean intensity) to visualize which wells are active. This view is fully connected to your data exploration—adjusting a gate updates the plate view in real-time. You can also easily group files by well (e.g., negative controls vs. treatments) to isolate specific populations.

We have been working hard under the hood to take Cytely to the next level. We are currently in Alpha release a brand-new processing engine designed to handle massive datasets with ease, increasing performance by more than 10x on large datasets. This update ensures that even when analyzing tens of thousands of objects, the experience remains lightning-fast.

What shipped this week:

While the new engine has been the main focus, we’ve also released several quality-of-life improvements to the interface:

Data Toggling: You can now toggle specific data groups on and off. This allows for cleaner visualization when comparing multiple datasets, such as filtering out specific files to focus on a single experimental condition.

Enhanced Visual Feedback: We’ve updated the analysis nodes to clearly differentiate between "pending" (slow spin) and "calculating" (blue/fast spin) states, giving you better real-time insight into your analysis progress.

Streamlined Workflow Creation: When creating a new workflow from scratch, the first channel is now selected by default, removing friction and saving you clicks.

We are constantly working to make Cytely the most robust, data-driven environment for your microscopy analysis. We have rolled out three key updates designed to improve reproducibility and speed up your time-to-result.

Tweak your analysis workflow

For all newly analyzed datasets, you can now access the Workflow Builder view to inspect the exact logic behind your results.

This means you can now visualize the specific nodes (e.g., Gaussian filters, background segmentation, object measurement) used to process your images ensuring you have full transparency into how your data is being analyzed.

Replicate analysis with one click

Science relies on reproducibility. We have added the ability to replicate analysis workflows from previous experiments.

This means that if you have or get shared a workflow that worked perfectly for a specific assay (like a specific Phagocytosis or Transfection setup), you can now clone that exact logic and apply it to new datasets. This ensures consistency across experiments and saves you from reinventing the wheel.

Streamlined feedback for quicker workflows

Getting from raw image to data exploration should be seamless. We have improved the dataset submission process, making it easier to attach specific feedback and experimental context when you upload your images.

By providing detailed context upfront, you enable us to configure and deliver your bespoke analysis workflows significantly faster, letting you get to the insights sooner.

Log in today to try out the new replication features and see your analysis logic in action.

Cytely is now more powerful with three new features available to all users.

Support for multiple image formats

Cytely now supports Tiff, Zeiss, and Olympus file formats so you can seamlessly work with images from your preferred microscopy systems without conversion hassles.

Direct microscope control

With our new data-dependent acquisition (DDA) feature and direct Nikon JOBS integration, you can now control your microscope and capture images directly from Cytely. Allowing you to easily take high resolution images of cells of interest.

Precise population gating with polygon shapes

Create free-shape gates to define your exact populations of interest. Move beyond simple rectangular selections to gate the precise cell populations you need for your analysis.

These features are available now for all Cytely users. Just log in to app.cytely.io to try it out.