Create a new scene and use TileMapLayer as the root node.

In the Inspector locate the Tile Set property

Replace <Empty> with New TileSet

Use the Terrain.png tileset image located in the Terrain folder.

At the bottom of the screen

Click on the TileSet tab

Drag and Drop the Terrrain.png image into the Tiles window.

Accept the offer to recreate the Tile Atlas

Most of our tiles will be solid but, those in the top right corner will be special

They will allow the player to pass through them.

To achieve this we will use two different  physics layers on the TileSet. 

Expand the TileSet property

Under Physics Layer add TWO new Elements

The TileSet now has TWO different physics layers

Each layer will interact with the player differently.

Tiles on Collision Layer 2 will be solid ground tiles and we will rename the layer to reflect that.

Tiles on Collision Layer 3 will be pass_through tiles and we will rename the layer to reflect that.

The player will occupy Layer 1 and we will rename the layer to reflect that.

Click on the numbers to turn layers on and off as shown in the screenshot to the left.


EXPLANATION

Collision Layer 2 is ON and LOOKING for collision objects on

 Layer 1 (Player)

Collision Layer 3 is ON and LOOKING for collision objects on

 Layer 1 (Player)

Rename the layers as shown by clicking on the 3 dots and then Edit Layer Names

Return to the TileSet

Select the Paint tab

Under Paint Properties

Select Physics Layer 0

These are our solid ground tiles

Here we can adjust the collision polygon for each individual tile!

For our purposes we will simply leave the polygon as a square

and paint every tile except for our pass_through tiles as shown.

(Paint by clicking on each tile.)

Under Paint Properties

Switch to Physics Layer 1

Ensure that One Way is ticked

for each of the pass_through tiles.

Adjust the collision polygon

Paint the pass_through tiles as shown.

One Way Collision means that the player can collide with the tile from above

but NOT from below.

This allows the player to jump UP onto the tile from below with no additional code.