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StereoMap 4.0.0 (June, 2024)

STOmics official website

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Release Highlights

• New user interface enables image QC, manual processing, and visual exploration in one application.

• Open one .stereo manifest 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.

Release Notes ->

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System Requirements

Windows

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

Performance Notes

• When analyzing large datasets (100 k+ cells/bins), 32 GB RAM and a quad-core processor are highly recommended for optimal performance.

• When working with data on an external storage device, such as an external hard disk drive, the performance of the application may be risked by data transfer from the device, including slower I/O, heightened latency, and potential crash due to unexpected disconnection.

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Installation

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

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 Stereo-seq Image QC to convert the compressed TAR (.tar.gz) image file to the latest version.

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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.

You can turn on the auto-update option so that the application will check the new versions automatically in the background.

Saving Path

The default saving path is your installation directory, you may change it to your preferred location from Setting as shown below.

Microscope Settings

Tips:

If you do not change any settings of your microscope, the configuration information will remain unchanged. Save your microscope configuration while performing an assessment for later use.

Within the StereoMap Setting , there is a feature for saving the details of your microscope image acquisition setup as a configuration file. This configuration file can then be utilized in assessing the quality of images. Click Edit/Add under Microscope Settings to open configuration list.

You can add a new , modify an existing , or remove a microscope configuration from the list. The parameters that can be saved in the microscope configuration typically include:

• Config Name: The name of the configuration, which will be displayed in the selection list.

• Manufacture: The manufacturer of the microscope.

• Model: The model of the microscope.

• Objective: The magnification and numerical aperture of the objective lens used.

• Overlap: Overlap ratio between FOVs.

• Scale: The scale or pixel-to-micron ratio of the image. It is crucial for accurately converting image measurements into real-world units.

• FOV Width: The width of a image FOV.

• FOV Height: The height of a image FOV.

• Set as Default: If you want to set this microscope configuration as the default option.

Press the Confirm button to store your modifications to the Configuration list.

This list is then utilized in the first step of Image Processing when you upload a TIFF format image that requires quality check. You can access, add, or edit this list from Image Processing as well.