Resolution Pyramids
Stitch and view massive full-resolution images on a low-RAM computer
Note: Available in Huygens Professional only
Every microscopist knows that image files continue to grow in size. To view and stitch these datasets, downsampling or cropping is often required to fit within the limited memory capacity of a computer. Unfortunately, these steps result in the loss of image data and/or image quality
Huygens' new Resolution Pyramid file format in Professonal offers a solution. It enables the stitching and visualization of massive datasets—containing billions of voxels and hundreds of gigabytes of data—without compromising image quality. Even on low-end computers, large images can be opened, viewed, and stitched with ease.
How does it work?
Since even high-resolution monitors cannot display images at full detail, it is often more efficient to display a downsampled version. As you zoom in, the Resolution Pyramid seamlessly loads higher-resolution data only for the region of interest, keeping RAM usage to a minimum.
And there is no need to worry about losing data. Huygens Resolution Pyramid stores all image metadata and statistical information alongside the original full-resolution image and its downsampled versions. Both the full-resolution image and any downsampled versions can be extracted easily from the Resolution Pyramid file whenever needed (see below).
Always view the optimal resolution!
bypasses RAM limits with uncompromising detail
Hover over images to enlarge
RAM limit required down-sampling, degrading image quality
Hover over images to enlarge
Left: Using Huygens’ new Resolution Pyramid HDF51 file format .pyr.h5, you can save and view extreme large datasets with the precision they deserve. The dark gray triangle icons in the left Twin Slicer images indicate that they are part of a Resolution Pyramid file, and the highlighted layer shows what resolution level is displayed.
Right: Classical approach: If no pyramid file format is used, images may need down-sampling to decrease file size for viewing and further image processing, thus compromising image quality.
Exclusive to Huygens Professional from version 25.10
Contact us for options to upgrade your Huygens Essential to Professional!
Pyramids can be generated from many image formats2
Stitch extremely large datasets at full resolution
View images far exceeding a device's RAM
Save as Huygens’ .pyr.h5 format
Extract full and downsampled versions from the .pyr.h5 format
Compatible with our Slicers, Stitcher and Cropper. Contact us for questions
Notice: All Pyramid files can be viewed in the Huygens Professional Slicers. At the moment, any image file stitched by the Stitcher in Huygens Professional can be saved as a Pyramid file. Also, any images that can be opened in Huygens Professional can be saved to a Resolution Pyramid format. For larger files, see footnote2. Compatible features will soon be expanded.
Diagrams showcasing three scenarios with an oversized file
Huygens’ Resolution Pyramids work with the HDF5 based file format, which is saved on the computers storage and contains the same image at different resolutions. The bottom tier contains the full resolution image, but cropped into smaller chunks. Tiers above this contain down-sampled versions made of fewer and larger chunks. These down-sampled versions contain less true detail, but are smaller in size and appear just as detailed on a monitor (at the zoom levels they are displayed at).
No Resolution Pyramid: The image cannot be opened in Huygens if the device does not have sufficient RAM to fit it, and Huygens Resolution Pyramid option is not used.
Resolution Pyramid: Images can be stiched and/or converted into a Resolution Pyramid file. Huygens shows only what is needed to minimize RAM usage.
Extract from Resolution Pyramid: Individual resolution levels can be extracted and viewed or saved as is. Creates smaller file sizes than complete Pyramids, yet leads to detail loss when using a lower resolution.
How to create a Resolution Pyramid
We currently offer three ways to create Resolution Pyramid files: 1) open Professonal and navigate to File > Generate Resolution Pyramid. From here you can choose an image and save location for the conversion process (this conversion can use RAM and virtual RAM). 2) Any opened image in Huygens that fits in RAM can be converted by right navigating to tools and selecting the corresponding task bar icon. 3) Lastly, the stitcher comes bundled with an option to save the final output as a Resolution Pyramid, which can be saved to storage.
There is also the option to calculate a histogram from the original high resolution image. This option can be disabled to save time in the conversion process, but if so, will result in a file that does not yet have a histogram. One can always be calculated after conversion if needed.
How to extract single layers to single images
To extract a single image from at a specific resolution level, navigate to the main menu, where your Resolution Pyramid is loaded. From here you can right-click and use Extract Layer. This generates an image in Huygens that you can use for operations, or save as a standalone image e.g. as HDF5.
Compatability notice
To clarify, the Huygens Resolution Pyramid .pyr.h5 format is still exclusive to Huygens software. It is not compatible or interchangeable with other pyramid or HDF5 file formats yet.
Footnotes/References
- The Huygens HDF5 (Pyramid) file format is based on the Hierarchical Data Format version 5 (HDF5), which is an open source file format that supports large, complex, heterogeneous data. Huygens HDF5 stores extensive metadata information of all the supported microscope types, including STED, Light Sheet and Array Detector based systems. For this reason, portability to other software may be limited. For more information, see http://www.hdfgroup.org/HDF5/ and FileFormats.
- Currently, all supported file types can be converted to a Huygens Resolution Pyramid file if they fit in RAM (+ virtual memory/swap space). For files that do not fit in memory, the list of compatible file types is still limited to: (Huygens) HDF5, ICS/ICS2, OME Tiff, OME, TIFF, Abberior MSR/OBF, Olympus VSI, Zeiss CZI, Leica LIF, LOF, XLIF, Imaris 5.5 HDF5 version. Attempting to convert non-supported files in Huygens will prompt you with a warning and bugreport option. This gives us insight on what formats to include support for in future patches.