Cytometry in R - Course Restarting Next Week

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Hello everyone, I hope that your summers are going well, and that you have found some respite from the temperature extremes everyone seems to be dealing with worldwide this month. Just writing a quick note to let you know that we will be re-starting the Cytometry in R course starting next week (Monday, July 13th).

This upcoming section will be primarily Spectral Flow Cytometry focused. This section will comprise of both primary course material, as well as bonus content.

The primary course material will be very similar to what you have experienced through the first third of the course. It's main purpose is to continue building your Cytometry in R skills by providing a broad detailed overview of the topic and making sure you understand the underlying concepts. For this section, this roughly equals breaking open what often from the outside seems like a black box (single-colors go in, something happens, out returns unmixed .fcs files).

The bonus contents focus is different, being more toward the implementation. It is aimed at providing a framework to allow you to readily implement unmixing in R as part of your regular workflow, without diving too far down into the underlying mechanics. Both primary and bonus content are meant to complement each other.

For this sections primary course material, we will be covering:

• "Week 12" will cover how to extract fluorescent signatures from our unmixing controls (single-color and unstained).
• "Week 13" focuses on comparing these fluorescent signatures via various metrics, including similarity (cosine), panel complexity (kappa), and unmixing-dependent spreading (collinearity).
• "Week 14" revolves around unmixing, with the goal of demystifying what often seems like a black-box.

And for the bonus material, we will be covering:

• Downloading datasets from ImmPort
• Pre-processing for signature extraction
• Assembling signature matrices
• Identifying problematic single-color controls with Luciernaga
• AutoSpectral
• TRU-OLS

The primary course material will be offered in the regular format:

For those attending online, our YouTube live-streams will be on:

• Tuesday 2200 EST (Wednesday 0200 GMT+0)

• Wednesday 1530 EST (Wednesday 1930 GMT+0) (except not this week due to the World Cup)

• Thursday 1000 EST (Thursday 1400 GMT+0).

All recordings will be available immediately afterwards on YouTube.

For those in Baltimore attending in-person:

• We will meet on Thursday at 4 PM EST (Bressler Research Building 7-035).

Most of the bonus content material is already available via our website. For the recordings, they are most likely going to be done as a single live-stream, with the recording available immediately afterwards (more details on the days and times next time).

Separately, I have only had time to verify that the code works on our Cytek Auroras. If you have a different spectral flow cytometer from another manufacturer, have some time to spare (and the interest to do so!) if you could check and let me know whether the bonus content workflow roughly works for your respective instruments or needs modifications, I would greatly appreciate it!

That is all for now, more details next week.

Best Wishes-
David