Tutorials

We're working on it! Hopefully these won't take tooooo long.

Tutorial 1: Something cool

This is a short description of what is covered in this tutorial.

The tutorial contents will go here!

Tutorial 2: Viewing point spectra and caterpillar plots

This is a short description of what is covered in this tutorial.

The tutorial contents will go here!

1. Drag and drop the files with the extension ".hdr" in the Napari interface.

2. On the left side of the screen, above the just added layers, select the points option to create the points layer:

3. Add points by selecting "+" on the upper left side of the screen:

4. Go to “Plugins” > “Hippo” > “Caterpillar”:

5. On the upper left side corner of the screen, in "Spectral Caterpillar", select the range/ plot you would like to visualise:

6. Keep adding other plots and adjust their hight and width by dragging the 3 small dots on the side and top of each plot:

Tutorial 3: Something even more cool

This is a short description of what is covered in this tutorial.

The focus should be on ensuring no background is included in the mask rather than covering all of each piece of the image dataset.

The tutorial contents will go here!

Tutorial 4: Quick'n'dirty masking

Masking or labelling N-D hyperspectral imagery can be done with hippo. Generally, you should use it to generate conservative masks (i.e., it is good to miss the edges of the image, but background pixels should certainly not be included in the mask).

The focus should be on ensuring no background is included in the mask rather than covering all of each piece of the image dataset.

1. Go to “Plugins” > “Hippo” > “Input / Output”:

2. On the right side of the screen, in “Choose directory”, select the folder where your .png files are located. To ensure that all .png files in the folder are uploaded, use “**/*.png” as the filter. Make sure that the options “rbg only” and “stack” are the only ones selected. To upload the files, click “Search”:

3. To upload all masks, use “filename” as mode and click “Load Masks”:To upload all masks, use “filename” as mode and click “Load Masks”:

4. To exclude a portion of a mask, select the “Exclude” layer on the left side of the screen, use the polygon tool to draw a polygon wide enough to cover the area to delete, and select “Update” on the right side of the screen:

5. To include a portion of a mask, select the “Include” layer on the left side of the screen, use the polygon tool to draw a polygon wide enough to cover the desired area, and select “Update” on the right side of the screen:

To save the masks, select “Save Masks” on the left side of the screen. This should update the envi files in the folder that was loaded.

• Due to a bug, napari shuts down occasionally. Make sure to save the masked files along the way.

Important commands:

1. Delete polygon,
2. Select and move polygon,
3. Select polygon and edit its points placement,
4. Create circular shape(e.g.,for small round masks),
5. Create rectangular masks,
6. Create polygon,
7. Draw polygon.

To Zoom In and Out, use the mouse wheel. By holding the space bar on your keyboard while selecting and holding a point in the image, you can move the image while in zoom-in mode.

Tutorial 5: This is a bit less cool

This is a short description of what is covered in this tutorial.

The tutorial contents will go here!