Release Notes for StereoMap
4.3.0 (March, 2026)
Visual Explore
Introducing the All-New Visual Explore! The redesigned user interface offers improved visuals and a more organized workspace, enabling more efficient data analysis.
The new interface is now divided into four main sections:
Display Mode: Includes Feature, Group, and Selection, which control how the data points are colored or grouped. The new Selection feature allows filtering of coordinate bins based on Group or Feature. After filtering, the retained bins can be saved as a new Group for further analysis.
Layer Panels: Includes Bin Layer, Cell Layer, and Image Layer. You can stack these layers and adjust their opacity for co-visualization of spatial feature expression matrices and images.
Workspace: The main area where the dataset is visualized.
Data Panel: Displays tables and charts for data analysis and interpretation.
New Feature: Projection. The Projection feature has been added, allowing visualization of different spatial projections for one or more chip datasets. It also supports UMAP visualization of cell bins.
New Feature: Split View. The Split View feature enables users to divide spots/cells based on selected labels or clusters into multiple independent subplots for visualization. This facilitates intuitive visual comparison of expression differences or grouping patterns across subplots. It supports division in both Projection Spatial and UMAP.
New Feature: Annotation Shape. The Annotation Shape feature allows you to create and temporarily store multiple lasso shapes during dataset analysis. This enables repeated extraction of spot coordinates or feature spatial expression matrices at different resolutions (bin sizes) for a specific region. Additionally, these lasso shapes can be exported as a
.geojsonfile for easy re-importation in future analyses.Effortless Region Selection & Export. With the lasso tool, you can select an area and save the spots or cells within it to a Group. From there, you can export the coordinates of the bins as a
.csvfile or export the matrix in.gefor.gemformat for further analysis.New Feature: Local Analysis. New local clustering analysis and differential analysis features have been added, utilizing local resources without requiring SAW (if resources are sufficient). This enables you to independently perform complex data analysis tasks in a local environment, further enhancing flexibility and autonomy in data processing.
Enhanced Color Adaptation.
The default heatmap coloring now adapts automatically based on the image type for improved visual presentation. Additionally,The default cluster coloring has been optimized for better readability in light UI mode, enhancing the overall visual experience.Visualization Screenshot Upgrade. The screenshot feature has been enhanced with a new background-free download option for improved flexibility in image export.
Multi-Window Linking: Now, links are based on spots/cell groups and features.
New Feature: Support for
SAW aggroutput.stereofile to display the aggregated slice analysis result. Added Across Multiple Samples form, enabling CSV output for differential expression analysis inSAW reanalyze diffExp, which analyzes expression differences between different slices within selected regions.
Image processing
Step 2: Enable the entire chip matrix (if recorded in
.stereo) to be displayed during morphology registration. Added matrix bin size adjustment.
Tools
Release a new tool: Manual Alignment! You can align multiple images by marking points.
4.2.2 (December, 2025)
Image Processing:
Fixed an issue with the expression matrix display in Step 2 Image Registration when Step 1 uses .stereo files as input.
Fixed an issue where image pyramid generation failed in Step 1 when the large input file was stored on a remote disk.
System: Fixed an issue with reading remaining disk storage on MacOS.
4.2.1 (November, 2025)
Image Processing: Bug fix to enable Feature Point Registration when processing images with SN ending in AA~PE.
4.2.0 (September, 2025)
Visual Explore:
When the number of spots is too large (bin1, or bin5 on chips ≥ 2×2 cm), the software automatically reduces the displayed spots to accelerate rendering. You can adjust the reduction ratio or disable this behavior in Layer Menu > Display Options > Level of Detail in heatmap view settings.
Image Processing:
Step 1: No need to enter microscope parameters when uploading QC stitched images.
Step 2: Added matrix transparency adjustment for morphological registration.
Step 4: Added new automatic model segmentation option for cell segmentation.
Added dashed box to indicate valid spatial matrix area in Steps 2, 3, and 4. Note: regions outside the box will not be recorded.
Tools:
Image QC no longer requires microscope parameters for stitched images.
In DAPI + mIF QC, calibration evaluation results are no longer a deciding factor for QC pass/fail.
Removed QC adaptation for multi-channel fluorescence images.
4.1.2 (March, 2025)
Resolved an issue where certain spatial feature expression matrix files failed to load in Step 2 of Image Processing.
Fixed incomplete display of the heatmap for Bin 1 in Visual Explore.
Fixed a bug where deselecting a protein in Stereo-CITE data caused linked windows to omit marker gene displays in Visual Explore.
Addressed an error where adjusting expression heatmap opacity incorrectly updated the MID filtering maximum value in Visual Explore.
4.2.0 (September, 2025)
Visual Explore:
The Level of Detail technique is automatically applied to bin1 (always active) and bin5 (when chip size exceeds 2×2cm) to accelerate heatmap rendering through detail reduction. To enhance visual fidelity, users can adjust the Level of Detail slider under Layer Menu > Display Options in heatmap view.
Image Processing:
Step 1: No need to enter microscope parameters when uploading QC stitched images.
Step 2: Added matrix transparency adjustment for morphological registration.
Step 4: Added new automatic model segmentation option for cell segmentation.
Added dashed box to indicate valid spatial matrix area in Steps 2, 3, and 4. Note: regions outside the box will not be recorded.
Tools:
Image QC no longer requires microscope parameters for stitched images.
In DAPI + mIF QC, calibration evaluation results are no longer a deciding factor for QC pass/fail.
Removed QC adaptation for multi-channel fluorescence images.
4.1.2 (March, 2025)
Resolved an issue where certain spatial feature expression matrix files failed to load in Step 2 of Image Processing.
Fixed incomplete display of the heatmap for Bin 1 in Visual Explore.
Fixed a bug where deselecting a protein in Stereo-CITE data caused linked windows to omit marker gene displays in Visual Explore.
Addressed an error where adjusting expression heatmap opacity incorrectly updated the MID filtering maximum value in Visual Explore.
4.1.1 (November, 2024)
To prevent any interruptions, the tooltip information of the spot is be hidden during lasso selection in Visual Explore.
Enhanced the user experience when viewing the bin 1 matrix in Visual Explore. The optimized viewing experience is now smoother.
Changed the resolution of the feature expression matrix from bin 20 to bin 10 in Step 2 Image Registration of Image Processing.
Added the notification displaying the saving path for the registered TIF image during the export process in Step 5 of Image Processing.
Adaptation of the new system! The first version of MacOS is released.(December, 2024)
4.1.0 (September, 2024)
You can now visually explore the distribution of an individual or selected feature at cell-level resolution.
For the Stereo-CITE dataset output by SAW version 8.1.0 or higher, you can easily visualize proteins and their corresponding marker genes in the linked windows.
When exporting files from Visual Explore or Image Processing, you’ll be prompted to choose a save location and file name.
New image registration method! Align images with the spatial feature expression matrix by marking a specific feature point. There is no need to import the matrix but ensure your image passes QC and the four chip edges or corners are visible.
Adds brief instructions to key steps of the Image Processing.
The image clarity assessment has been removed from the Image QC process.
After the Image QC progression is completed, the saving path information is now included in the QC result suggestion section for improving information delivery. Clicking the path will open the file system and navigate directly to the folder.
4.0.1 (July, 2024)
Fixed several known issues.
4.0.0 (June, 2024)
New entrance interface for Visual Explore, Image Processing, and Tools.
Open one
.stereomanifest file in the SAW-generated bundle file for visualizing any datasets. No need to understand the correlation between visualization and the content of each file.Adds functionalities in Visual Explore for manually labeling regions and organizing labels into groups.
Select label group and "Export differential analysis file" to set parameters export to the differential analysis pipeline in SAW.
StereoMap introduces a redesigned Image Processing tool to enable more accurate segmentation of Stereo-seq image data before exporting to SAW. This update includes:
New and improved user interface for processing images in a list of recommended steps.
Support for uploading segmentation binary
.tifimage results generated by any applications or algorithms at the tissue segmentation and cell segmentation steps. The uploaded segmentation binary result will be passed into SAW for extracting the tissue/cell matrix.
The Image Processing steps also include an image registration step, which allows for manually aligning a Stereo-seq image with a spatial gene expression matrix.
Introduction of Image QC tool for evaluating image quality. The image passed QC can be auto-processed by SAW, otherwise, needs to be manually processed using the Image Processing tool.
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