Feature Ideas

As a user, I would like to be able to precisely and in an easily repeatable manner apply the exact same gating strategy by manually entering data. Solution Allow users to set or edit the bounds of a gate numerically by manually entering coordinates instead of only using visual selection tools.

As a user, it can sometimes be hard to see a population of interest due to the scaling of the axis. The most intuitive would be if one could zoom on the plots. We should add the ability to zoom in plots. Solution Acceptance criteria: Scrolling in the scatter plot now zooms the viewThe axes are updated accordinglyThe brush is updated accordinglyIt is highlighted that a zoom has been appliedThe zoom state is re-applied on page refreshes (store in brush on BE?)

As a user navigating the population overview, I want panning to be constrained to the data area so I don't scroll into empty space. Solution Constrain panning to data bounds (prevent scrolling into empty space beyond where cells exist).

As a user, I want to explore differences between different sub-populations by being able to apply multiple gating strategies to the same data. As a user, I want to be able to apply multiple gates in one graph and combine them as a single population. Solution Enable users to: Select multiple places in one graphGroup data by selecting regions and combining themApply multiple gating strategies to identify sub-populations

As a Biomedical Researcher comparing different conditions, I would like to use the group buttons above the scatter plots to show or hide specific cell populations, so that I can focus on specific data subsets without visual clutter and analyze only parts of my data. 💡 Proposed Solution Make the group identifier buttons (located at the top of the scatter plots) interactive and change how they work from being only an image organization tool to being a gated collection of cells. Clicking a button should toggle the visibility of that specific group within the scatter plot.

I would like bidirectional interaction between cells and visualizations: Click a cell thumbnail or a datapoint in a gating graph to locate and inspect that specific cellClick a cell on the map and see it highlighted in the plots This allows me to identify cells in my sample, in my gates, and understand the relationship between spatial location and measured parameters. Solution When clicking a cell thumbnail OR a datapoint in a scatter plot/gating graph: Highlight the associated thumbnail (if part of the gated population)Zoom the map to center on that cell's locationOpen the cell preview panel showing the cropped cell image with all channels When clicking a cell on the map: Highlight it in the scatter plotsApply the same color highlighting in both the mini map and the plots

As a user viewing a cell preview in the Data Explorer, I would like to quickly navigate to see the full raw image in the Images tab so that I can see the cell in the context in which it was captured. Solution: Add a link or button in the cell preview panel (when viewing a cropped cell) that navigates to the Images tab and: Opens the corresponding full image fileCenters/highlights the selected cell in that image view This allows users to seamlessly move from analyzing individual cells in scatter plots to viewing them in the context of the complete microscopy image.

Saving commonly-used gating strategies and plot configurations as templates would enable quickly applying them to different datasets. When working with similar experiments, recreating the same gating strategies and plot configurations for each new dataset is time-consuming and error-prone. It would be helpful to be able to save gates and plots as named templates and apply templates to new datasets.

Exporting thumbnails with scale bars and choosing between current or original lookup tables would help with publications.

Plotting data in log scale would enable better separation between populations for analysis.

Fullscreening the plot section in Data Explorer would enable viewing scatter plots in a larger workspace for better analysis.

Saving thumbnails either individually or exporting all at once would help with documentation and presentations.

Analyzing multiple types of sub-objects (e.g., object A, object B, and their overlap) within the same parent cell requires multiple child masks.

Opening selected microscopy images in a full-screen overlay would enable inspecting cellular details without being limited by a small side panel.

Researchers unfamiliar with image analysis need simple definitions of parameters like 'Circularity' or 'Major Axis Length' to understand their data.