Add your own slides

When opening the microscopy module, you can as Admin add your own microscopy slides.

First, you need to create a track (folder) to add your slide(s). To do so, click on "Create New" in Add New box to be redirected to the Create a new track page.

In this page you can name your track and write a description for it. Also, you will be able to upload a thumbnail and see its preview. The thumbnail helps you to recognize your track faster when it is placed among many other tracks. When you did all you did all these steps, you need click on Save Changes to create your track.

Once you save your track, you will be redirected to the track page and you can see the created track. By clicking on Edit you can modify properties that you assigned, duplicate, or delete the track. By Clicking on Open, you will be redirected to a new page where you can Export the microscopy images. 

Here you can Export the slide(s) to your track or see the slides that have been already exported. To export new slide you need to click on Export button on top left.

By clicking on Export button you will be redirected to a new page which is as same as Create plot page. To get the options related to microscopy module, you need to select Pathology Slide as the algorithm. 

The regarding options are expressed in two separate menus named Select Review Template and Cells Types and Slide Metadata.

Select Review Template and Cells Types 

In this menu, you see four separate items:

1. Select Review Template: Choose the tissue type the from which the microscopy slide was obtained.
2. Select Slide: Select the slides you want to analyze in your study through the drop-down menu
3. Select Cell Types for Counting: On the Slide Image, you are able to count the cells. This item allows you to specify cell types you want to be counted on the slide image.
4. Classification Type: This item allows you to specify which type of cell classification you want to implement in your microscopy module. There are three types of cell classification on this matter:

• Free cell classification: Trainee can make all changes in this module.
• Fixed cell classification: Trainee can change the names of the markers in this module.
• View-only: Trainee cannot make any changes in this module.

Slide Metadata

In this menu, you can write the metadata information including, Demographics, Physician Request, History, Physical Exam, and Lab Results of the case the sample was obtained.

After you put in all the data, you can temporarily save all the info by clicking on the Save Placeholder or create the microscopy module by clicking on Run. The buttons are located on top left.

By running the project, you will be redirected to the track page and can see the project just created. Click on the Select below the case to see a new pop up window will appear on the left. By Selecting View Interactively, the microscopy module will be opened.

Once you are on the Microscopy module page, you will notice that it consists of two sections:

• Slide image (3.1): This is the image of the slide that visualizes the cells.
• Slide metadata (3.2): This is the side panel on the left. It gives information on the case, the slide image and the cells.