The Stereo-seq chip mask file stores a list of all known CID (Coordinate ID) sequences, which are crucial for mapping spatial information. Each CID corresponds to a unique spatial position on the chip, allowing researchers to precisely locate where each sequence originates. This spatial mapping is essential for understanding the spatial organization of cells and tissues, which can provide insights into cellular functions, interactions, and the overall architecture of the biological sample.
Stereo-seq chip diagram
Each Stereo-seq chip mask file corresponds to one physical chip. Be sure to use consistent files during analysis. The mask file name format is shown below.
Stereo-seq chip mask file name format
Where to Find Chip Mask
Accessing the DCS Cloud platform
STOmics Tech. utilizes a cloud-based platform, DCS Cloud, to store and transfer your Stereo-seq Chip Mask file. You can find and download your Stereo-seq Chip Mask file from the DCS Cloud platform.
Once you have purchased Stereo-seq kits, your order will be connected to DCS Cloud. To obtain your mask file, you will need to register for a DCS Cloud account on your region's website. If you are unsure about the correct site or have questions about the cloud or data center, please contact your local sales representative for assistance.
For American region, please contact your local representative via Email (STOmics-support@completegenomics.com) for assistance.
Quick Download (ordered through MGI)
If your product was purchased throuogh MGI, we recommend accessing the file download interface from the DCS Cloud homepage. To do this, navigate to "Public resources" -> "The mask of chip" on the right side. This method allows you to download the mask files directly without having to wait for your account to be added to a project.
You can easily download the chip mask files by entering the Stereo-seq chip serial number (SN) found on the back of the chip. Alternatively, you can use the serial number of the Stereo-seq Slide kit. This kit serial number consists of the product reference number (REF) and the serial number (SN) found on the label of the box. Please note that when entering the REF and SN together, there should be no spaces in between.
Quering by Stereo-seq chip SN
Quering by Stereo-seq kit serial number (REF+SN)
Quick Download (Install download_mask Tool)
Another convenient option is to use the download_mask Tool to obtain mask files. This method requires no DCS Cloud login or token verification. Simply enter the Stereo-seq chip SN or the Stereo-seq kit serial number (REF+SN, entered without spaces), and the files can be saved directly to your local machine or Linux environment.
Download mask by Stereo-seq kit serial number (REF+SN)
Regular Download (download files from "Data" of the project)
You can download your mask file as a regular file. All files on DCS Cloud are organized within a "Project." If your account has been added to a project, you can access your mask file from there.
When logged in to the DCS Cloud site, find your project from the menu or by using the "Recent project" quick start option.
DCS Cloud home page
After entering the project, navigate to the “Overview” section. All raw data and analysis results are stored under “Data”. Click on “Data” in the sidebar to access it. To locate the Stereo-seq Chip Mask files, select the “h5” file extension. If you need to find a specific Stereo-seq Chip Mask file, use the serial number (ID) located on the back of the chip or the number on the label of the Stereo-seq Chip Slide package.
Access the "Data" project and filter for files with the "h5" extension.
Locate the mask file for a particular chip by using its serial number (SN).
How to do a Regular Download
Option 1: Web download (Alibaba & AWS Cloud)
For projects deployed on Alibaba or AWS Cloud, a "Web download" option is available for downloading files. Just select the mask file, click "Web download," and the file will be transferred to your device.
Option 2: Raysync download (Shikong Center)
Mask files in data center are stored on internal servers, like HPC. Due to security concerns, transferring these files from the internal server to the publicly accessible network requires passing through a DMZ buffer zone and firewalls. Therefore, when downloading a mask file from data center, especially Shenzhen, you will need to first "transfer" the file from the internal server to the DMZ and then "download" it to your local file system via the Internet.
Step 1: Transfer your mask file from the internal server to DMZ
For projects created within the last 3 months, you can skip this step. Your mask files have already been transferred and are temporarily saved on DMZ servers.
Step 2: Download the mask via the Raysync tool
Raysync offers two methods for downloading files: using the Raysync client application or command-line tools.
When using Raysync client, you may be prompted to download and launch the Raysync client if it's not already installed. Once installed, launch the Raysync client application, return to the web interface and click "Download" button for your desired file. The client will handle the transfer process.
When using Raysync command-line tools, download and install the tool suitable for your operating system. Ensure that the necessary environment variables are configured correctly.
In the web interface, click "Generate and copy download command" to obtain the command tailored to your selected files. Determine and specify the directory where the files will be saved, and execute the generated command in your terminal or command prompt to download the files to your local or cluster environment.
Note: Each time you click the "Generate and copy download command" button, it may incur additional charges.
Option 3: Ossutil tool download (Alibaba Cloud)
The Ossutil tool is a command-line utility provided by Alibaba Cloud for managing their Object Storage Service (OSS). The tool is compatible with Windows, Linux, and macOS.
Step 2: Copy and paste the auto-generated command and download the mask file from the cloud
Windows: paste commands to console
Linux: add ./ and paste commands to console
macOS: paste commands to terminal
Option 4: AWS CLI tool download (AWS Cloud)
The AWS Command Line Interface (AWS CLI) is a unified tool to manage your AWS services from the command line. The tool is compatible with Windows, Linux, and macOS.
Step 1: Install AWS CLI
Windows: double-click .msi file to install AWS CLI
Linux: follow README.md to install AWS CLI
macOS: double-click .pkg file to install AWS CLI
Step 2: Copy and paste the auto-generated command and download the mask file from the cloud
## Linux version
./download_mask download -h
## Windows version
./download_mask.exe download -h
## Linux version
./download_mask download -c <Stereo-seq chip SN>
## Windows version
./download_mask.exe download -c <Stereo-seq chip SN>
## Linux version
./download_mask download -b <Stereo-seq kit serial number (REF+SN)>
## Windows version
./download_mask.exe download -b <Stereo-seq kit serial number (REF+SN)>
