StereoMap
Due to changes in third-party server services, the upload function following image QC (quality control) in previous versions (StereoMap 4.0 & 4.1, ImageStudio 3.0) may encounter connection issues or failures. As a result, the embedded Raysync upload path within the software requires modification. For specific details regarding the update patch, please refer to the Patch_UploadConfiguration_202506.
This update does not affect other major features of StereoMap and ImageStudio. If you do not need to upload files after image QC, you may choose to skip this update patch. We apologize for any inconvenience this may cause and appreciate your understanding and support.
StereoMap 4.2.2 (Dec., 2025)
StereoMap 4.2.2 highlights:
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.
StereoMap 4.2.1 (Nov., 2025)
StereoMap 4.2.1 highlights:
Image Processing: Bug fix to enable Feature Point Registration when processing images with SN ending in AA~PE.
StereoMap 4.2.0 (Sep., 2025)
StereoMap 4.2.0 highlights:
Visual Explore:
When the number of spots is too large (bin1, or bin5 on chips larger than 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.
StereoMap 4.1.2 (Mar., 2025)
StereoMap 4.1.0-4.1.2 highlights:
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.
The image clarity assessment has been canceled from the Image QC.
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).
Resolved an issue where certain spatial feature expression matrix files failed to load in Step 2 of Image Processing.
StereoMap 4.0.1 (Jul., 2024)
File size: 622.3M
md5: 98af09d8ea87f0faa3109fc7f17b8deb
StereoMap 4.0.0-4.0.1 highlights:
New user interface enables image QC, manual processing, and visual exploration in one application.
Open one
.stereomanifest file for visualizing any datasets.Manually label regions of interest and organize labels into groups.
Export differential expression analysis parameters to SAW, and import results for visualization.
Manually processing images in a list of recommended steps.
StereoMap 3.1.3 (Jul., 2024)
File size: 216.6M
md5: 9e0dab99b60060d72499abf3b982ab74
StereoMap 3.1.1-3.1.3 highlights:
Supported for visualizing Stereo-CITE dataset. You are allowed to visualize spatial protein heatmap and clustering result in spatial and UMAP projection for both binN and cell resolution.
You can open a linked window to display the gene and protein expression maps side by side. The canvases are connected by corresponding spots. For instance, when you select a cluster in one window, the related spots in the other window will also be highlighted, retaining their original colors, as they share the same coordinates. Additionally, you can use the lasso tool to create this effect.
Expression data for selected genes or proteins can now be filtered by MID. The adjusted MID range can be exported to a JSON file, imported into SAW, and then exported as a final gene or protein GEM file.
Added a new distance measuring tool.
Fixed the issue that the registration template cannot be displayed.
Fixed the issue of exporting lasso JSON.
End of Support
The following software versions have reached End of Support status. We will no longer provide technical support, bug fixes, feature updates, documentation updates, or compatibility assurance. While your current software may continue to function, we strongly recommend upgrading to the latest version. New versions are fully compatible with all Stereo-seq kits and designed to meet current demands.
StereoMap 3.0.2 (Nov., 2023)
File size: 201.4M
md5: 5f778386cc4f78591ea32ec23ff0c5c8
StereoMap 3.0.0-3.0.2 highlights:
Supported for visualizing Stereo-seq FF + H&E data.
You can now visualize the cell bin heatmap!
You can upload H5AD files with different bin sizes. When you select a specific bin size, the Cluster option in the Main Analysis Layer will be enabled to choose, and you will see the clustering result.
StereoMap 2.1.1 (Jul., 2023)
File size: 183.7M
md5: b624ef503528bf7d5f1f5f7540cb87c2
StereoMap 2.1.0-2.1.1 highlights:
Supported importing unaligned image
fov_stitched.rpifor manual registration. The registration parameters can be later utilized in SAW for image processing and to re-extract the gene expression matrix.Supported inputting multiple square bin GEFs, especially those with the
.label.gefextension. These matrices will be listed in the Main Analysis Layer panel, allowing for exclusive visualization of each one.Fixed the issue of image registration.
StereoMap 2.0.3 (Feb., 2023)
File size: 193.8M
md5: f8e8e1989d99afd4ece4dfbf72269e34
StereoMap 2.0.0-2.0.3 highlights:
Supported for visualizing Stereo-seq FF + mIF data. You can now visualize DAPI (in blue) alongside up to six immunofluorescence (IF) images, all aligned with the gene expression matrix. The images are listed in the Image Layer panel. Each IF image is a single-channel grayscale image, and you can change the colors for these images. You can display all the IF images together to observe their relative positions.
You can store your adjustments to a JSON file and then reload configurations to restore your previous settings.
Supported for using lasso tool on cellbin layer.
StereoMap 1.0.0 (Feb., 2023)
File size: 181.2M
md5: 843e0d53ef65c5534a7c8ff97a20caff
StereoMap 1.0.0 highlights:
The initial release of the Stereo-seq desktop application for interactive visualization.
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