Submitting Spatial Transcriptomics Images

Spatial Transcriptomics image submissions use the Fluorescence In Situ Hybridisation (FISH) standard to describe the experimental context, imaging parameters, probe information and spatial relationships required to interpret gene expression patterns within tissue sections.

Prerequisites

Important

  • This section applies if you are submitting images to a Biodata profile [1]. For sample image submissions under Tree of Life (ToL) [2] profiles, see Uploading Sample Images section.

  • A Biodata profile is needed to proceed with this section. Refer to Steps to Create a Biodata Profile to create one. Skip this step if you have already done so.

Note

Accessing the Images Page

Create a profile following the steps in Biodata profile creation. Then, access the Images page via any of the following methods:

Using the Components Button

  1. Click the images-component-button-st-fish component button in the Components column as shown below:

    Images profile component button

    Button to access the Images page (highlighted)


  2. Select Manage Spatial Transcriptomics images option to navigate to its page:

    Image subcomponents indicating 'Manage Spatial Transcriptomics image' option

    Dropdown menu showing Spatial Transcriptomics images option


Using the Components Icon Navigation Pane

The component icon navigation pane provides a quick access to other components associated with the same profile. It appears on the inner right pane of the screen when you are viewing a component’s page. The icons displayed in the navigation pane correspond to the components associated with the profile.

If you are unsure what each icon represents, you can perform any of the following:

  • Hover over the icon in the component icon navigation pane to see a tooltip with the component’s name

  • Refer to the component button image above

  • Refer to the What are profile components? FAQ

Note

  • The navigation pane will not display the icon associated with the page that is currently being viewed.

  • If a component has subcomponents, a dropdown menu is shown when at least two items are available. However, if you are viewing a subcomponent’s page and only one item remains, that item is displayed directly in the navigation pane.

Images profile component icon

Navigation pane showing the Images icon

Clicking the Images component icon in the navigation pane will display a dropdown menu with the available subcomponents as shown below:

Spatial Transcriptomics image profile component icon subcomponent

Navigation pane showing Spatial Transcriptomics image icon

Upload images

  1. Click the dropdown menu to choose a checklist [3].

    Pointer to Image checklist dropdown menu

    Pointer to dropdown menu for images


    Hover over each option to view its description. An overview of each option is provided in the Image Manifest Checklists section.


    Available image checklist options within a Biodata profile

    Checklist options for image submissions


  2. Click the images-blank-manifest-download-button-st-fish button to download a blank manifest [4].

    A manifest is a spreadsheet file used to record metadata for submission.

  3. Fill in the downloaded manifest then, click the add-images-manifest-button-st-fish button to upload it from your local (computer) system.

    Please ensure that the manifest that you are uploading matches the checklist type selected in step 1. You will encounter errors if the uploaded manifest does not correspond with the selected dropdown menu checklist option.

    Pointer to 'Add study from spreadsheet' button

    Click “Add study from spreadsheet” button to open an upload dialogue


  4. A dialogue is displayed. Click the images-upload-button-st-fish button in the dialogue to choose the spreadsheet file from your local system.

    Upload images spreadsheet dialogue

    Click ‘Upload manifest’ button


  5. The uploaded data is shown in a preview before final submission. Click the images-finish-button-st-fish button to finalise the upload.

    Dialogue with uploaded image data

    Images upload preview


  6. The new image data will be displayed on the Spatial Transcriptomics images page after a successful validation.

    Image data uploaded

    Images page showing the uploaded data


Submit Images

Note

  • Follow the steps in Upload images to upload data before proceeding with the submission.

  • The following repositories are supported for image submissions:

    • European Nucleotide Archive (ENA) via submit-record-button-ena button

    • Zenodo via submit-record-button-zenodo button

  1. After uploading data, select a row in the data table under the STUDY tab.

    Then, click the submit-record-button-ena button to submit the selected record to ENA or submit-record-button-zenodo button to submit to Zenodo.

    Hint

    The first row of the data table under the STUDY tab is selected by default. Selected rows are indicated by a blue background colour.

    Note

    Please ensure that the selected record is under the desired checklist option. If not, choose another option from the dropdown menu, then select a row in the data table.


  2. Wait for the submission process to be completed. The submitted record’s status and accessions can be viewed in the data table’s respective columns. See the sections below for details.


Make Data Public

  1. Submissions are private by default. You can make the data publicly accessible by referring to the steps in the Publishing Data at Data Level section.

View Submission Status

Hint

The Data status & progress legend, located on the right side of the data table, shows the different stages of submission processing. Hover over the info-icon to see description for each status.

For more details, see the How can I check the status of my data submissions? FAQ section.

The submission will be scheduled for processing after the submit-record-button-ena or submit-record-button-zenodo button is clicked. The row of the submitted record will be highlighted in green indicating that the submission has been successful.

If the submission was unsuccessful or has not been assigned any accessions, the table row will be highlighted in red. Its status is indicated in the following columns:

  • Status for Ena - Displays the ENA status assigned to the project

  • Status for Zenodo: Displays the Zenodo status assigned to the project

View Accessions

Accessions are unique identifiers assigned to submissions after they have been successfully submitted to public repositories.

The accession columns are:

  • Accession for Ena - Displays the ENA accession assigned to the project

  • Accession for Zenodo: Displays the Zenodo accession assigned to the project

Clicking any accession in the data table will open the corresponding record in the associated repository. You can also find the same record by searching for the accession directly in the repository.

Tip

Alternatively, click the accessions-component-icon icon located in the top-right corner of the data table to navigate to the Accessions page that displays accessions for all submissions.