syGlass End-of-Year 2025 Release: v2.5.0
2025 may be drawing to a close, but we at syGlass haven’t yet called it a year. This holiday season, we’re delivering support for lots of new file formats, alongside improvements to image visualization, segmentation, and narration creation.
Learn more about what’s new below, check out the full changelog, and don’t hesitate to send us a message for any assistance you might need in putting these new features to work for you.
Dynamic Depth Color Map Visualization
The “depth color map” visualization option in syGlass has historically encoded depth, in terms of the image stack’s z-axis, as color. syGlass v2.5.0 upgrades this behavior to instead use depth from the current viewpoint, meaning that things close to the view are colored differently from those far away from the viewer. This behavior updates the colors of structures in real time to allow for strong depth cues even during exploration of distant areas of an image.
The new dynamic depth map shown in action on a cleared mouse brain. Image data provided by Hsu et al., EZ Clear for simple, rapid, and robust mouse whole organ clearing (2022) eLife.
This setting can be particularly useful in combination with the existing “max intensity projection” (MIP) option. This option projects, in the current view direction, the highest-intensity portions of the image. This emphasizes bright areas, but can leave the viewer without strong depth cues; by using color for these cues, we can reap the benefits of max projection without sacrificing the ability to perceive depth.
Support for NRRD, MRC, TCF, and New Varieties of Zarr Files
syGlass accepts a wide variety of file formats for image data, and our coverage is still expanding rapidly. This release brings support for the NRRD and NHDR file formats used by 3D Slicer, Volume Graphics, and others; the MRC file format that is common in the worlds of cryoEM and ET; the TCF file format used by Tomocube; and lots of new flavors of OME-Zarr, including Zarr v3.
Improvements to the Narrator Experience
Text labels placed in syGlass can now be attached to the targeted structures via lines, keeping densely labeled areas visible.
v2.5.0 delivers lots of new features related to the creation of immersive narration content:
Avatar and microphone confirmations prior to recording
Text labels that can be attached to structures via lines
Visualization settings sliders now update in real time during narration playback
Improved audio quality for narrative content
Simple text slides, to be shown on the TV screens in the room, can now be generated directly in syGlass
Creating new narrations from existing ones is easier than ever: right-click an existing narration to bring the scenes that make it up back into the editor
Segmentation Improvements
There are plenty of reasons that performing 3D image segmentation in VR is advantageous: stereoscopic visualization gives you a unique perspective on 3D relationships in your images, and controllers tracked in 3D space allow for precise annotation in multiple image planes at once.
This process, in syGlass, is only getting easier. Mask colors can now be edited directly in VR. Mappings of mask IDs to names and colors can now be transferred easily between projects, allowing for similar segmentation schemes to be applied to many image volumes quickly. All syGlass-supported file formats can now be used to import mask data as well. And surface area and sphericity metrics are now exported alongside other mask statistics.
Editing colors assigned to a given mask can now be done directly in VR, just by clicking on the color swatch for a given mask.
… and Much More
There’s lots more to be excited about in v2.5.0, including other new features and many stability improvements and optimizations. You can read more about that in the full changelog, and then get in touch with us if you’d like to give it a try.
Four times a year, we’re here to deliver in-demand features and improvements, and that won’t be changing in 2026. We’ll be back soon with more exciting updates to start the new year.
