Tutorials

1. Introduction

The Navigation bar is located at the top of the website and includes the following pages: Home page, Chat with AI page, Image page, Image of FOV page, Gene Expression page, Enrichment page, and Differential Expression. You can click the corresponding link to access the desired page.

Home page: The main page of the website, offering a brief introduction to the platform and the database. It also features a chatbox with AI assistant.

Chat with AI page: A dedicated page for chatting with the AI assistant. It can answer questions about the website and generate images based on your queries.

Image page: Displays slide images and Field of View (FOV) information.

Image of FOV page: Showcases images of different FOVs, along with the corresponding conditions, samples, and associated gene information.

Gene Expression page: Displays gene expression data across different cell types.

Enrichment page: Highlights pathway enrichment across various cell types.

Differential Expression page: Presents differential expression data for cell types under different conditions.

There is also Help page and About page, which provide tutorials and basic information about the website.

2. Chat with AI

Type your question into the text box and click "Send" to receive an answer within a few seconds. You can also ask the AI assistant to generate images, supporting all types of images available on this website.

To clear the chat history and start a new conversation, click "Start New Conversation" in the top-right corner.

3. Image

On this page, you can view images of different slides and the locations of each FOV.

First, click on one of the four slides on the left to open a larger view. On the enlarged image on the right, you can zoom in or out using Shift + touchpad or Shift + mouse wheel, and move the image by dragging with the mouse or using the touchpad.

The yellow squares with numbers represent the FOVs. Click on any FOV square to open the Image of FOV page with the selected FOV displayed.

4. Image of FOV

On this page, you can generate images of different FOVs, either without genes or with specific genes. You can select a single gene or input two or three genes. However, if you input two or three genes, the process may take a long time. Please do this only when necessary. Once the image generation is complete, we will send it to you via email.

To generate an image:
    1. Select the condition, sample, and FOV step by step. Alternatively, you can click on an FOV square on the Image Page to have it
        automatically selected.
    2. Choose a gene option: None, Single, or Multiple.
            If you select Single, choose the gene from the dropdown list.
            If you select Multiple, input the genes (two or three) and your email address in the text box.
    3. Click Submit to generate the image. If the image is ready immediately, it will appear on the page; otherwise, it will be sent to
        your email.

5. Gene Expression

This page displays the expression of genes across different cell types.

To use this feature:
    1. Input the gene(s) in the text box, separated by commas (,) or new lines. You can input one or multiple genes.
    2. Select the cell type(s) by checking the box next to each cell type name. You can choose one or multiple cell types.
    3. Once you've made your selections, click Submit.

A progress bar will appear, and the resulting image will be displayed once the process is complete.

6. Enrichment

This page displays the enrichment of pathways across different cell types.

To use this feature:
    1. Select a pathway.
    2. Select a cell type.
    3. Click Submit.

The corresponding image will then be displayed.

7. Differential Expression

This page displays the differential expression of cell types under different conditions.

To use this feature:
    1. Select a cell type.
    2. Select a condition.
    3. Click Submit.

The corresponding image will then be displayed.