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StereoMap 4.3

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Download for MacOS

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StereoMap 4.3 highlights:

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: 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 .geojson file 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 .csv file or export the matrix in .gef or .gem format 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 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 based on spots/cell groups.

Release Notes ->

Previous versions ->

System Requirements

Minimum Requirements

Windows

Windows 10 or later (64-bit)
16 GB RAM (minimum 8 GB RAM for Tools-QC)
SSD storage highly recommended
100% scaling display setting recommended

MacOS

Compatible only with the Apple M-series chips
MacOS 11.3 (Big Sur) or later
16 GB RAM
SSD storage highly recommended
Default display settings recommended

Performance Notes

For large dataset analysis (100K+ cells/bins), 32 GB RAM and a quad-core processor are highly recommended for optimal performance.
When working with external storage devices (e.g., external hard drives), performance may be affected due to slower I/O speeds, increased latency, and potential crashes due to unexpected disconnection.

Installation

StereoMap for Windows is distributed as a self-installing executable (.exe) file. Double-click on the installation file to start installing.

If you encounter the following prompt during the installation, you can click "Open"，and add it to the trusted file.

Follow the prompts to choose an installation directory. The default directory is the local D drive.

Before you install, verify that there is enough disk space in the target directory. For both new installation and upgrade, your installation directory must meet the minimum of 20 GB of available disk space.

Avoid installing the application in a directory path that has special characters or symbols. The supported characters include space, underscore, letters A - Z, and numbers 0 - 9.

Compatibility with SAW

SAW >= v8.0 (compatibilty of history versions)
Re-run Image QC to convert the compressed TAR (.tar.gz) image file to the latest version.

Setting

Application Update

Click on the setting gear at the top right of the window to open the Setting page. Select About to get the version information and check the updates manually (internet required). If a new version is available, you will be asked to download and install a new package.