Instructor Notes

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There is a lot more information here that we have time for during the session so I would suggest going through these elements very briefly and/or skipping altogether. If they want to look at the challenges themselves after we can point that we will have them.

Skip this section on blending

Just go briefly over the types of layers

Mention that layers can be made up of different objects depending on what they represent. We are looking at an image but could annotate with points/shapes, and we will make a labels layer in our segmentations in a later episode.

Explanation on plugins

Explain that they will not be able to see the plugin explorer due to an issue where the micro-sam plugin seems to disable search for plugins through napari. Use a conda environment, tell them we have put alternative instructions to install in case you want to explore plugins but many would be available to install at command line, so we will go to napari-hub and show plugins page saying that this is what it looks like in case you want to try out later.

Highlight what to look for in a plugin

This section is good just to touch upon what to consider when looking at plugins. We won’t have time to do the challenge.

What is an image?

Working in the console

Instead of the notebook, use the console. And by sow that the layer can also be accessed via the name of the layer

This section is out of scope.

We don’t have time to cover this bit about creating an image.

Resuming teaching

The image dimensiosn bit is an important one

Go quickly through types

I don’t think we need to go through this. Look for a resume instructor note.

Resume just to cover common data types

That often we will see 8 or 16 bit, with float’s making sense in some cases as well. It’s all a tradeoff between precision needed and storage required. More bytes per pixel can store more values but will take more space on disk.

Briefly cover coordinate systems

Highlight that the information is there in Napari, and these can help access individual pixel values, make accurate measurements and perform spatial operations. THey are different from usual x and y axes in plots

Using Napari through Jupyter

Say you assume people have worked with Jupyter notebooks before

But if not, we will provide more of a primer in the materials at the end of the workshop.

Image Segmentation: Basic Concepts

Check time before going into smallest one

This and clear border will be nice to have, but you really need to get everything previously done efficiently.

Instructor Note

You may have to not go so forensically into which ball size to choose, depending on time.

Skip the for loops

Great for longer carpentries session where we have time to teach about code but not here.

Keep explanation about dilation brief!

Probably only time for a brief introduction into dilation being the reverse of erosion, with the expand_labels not allowing for stopping dilation if it hits another instance