Seminar 2: Defend Your Analysis

Friday 10:00–12:00 CEST · live on Zoom · mandatory.

The Friday seminar is where you defend the microscopy work you did in Wednesday’s computer lab. It is not a lecture and it is not a paper-reading club — you present your own image analysis, screen-share your interactive viewer, and the room questions it. The format is the same as every seminar in the course (weeks 1–6); this page tunes it to Week 2’s image work.

What the seminar is

This year the course trains you to be a forward-deployed scientist — to take someone else’s problem, direct an AI agent to solve it, and own every number that comes back. Owning a result means being able to stand behind it out loud, so the seminar is your own work, defended. This week the “result” is visual, so you don’t just talk about it — you show it on screen.

Think of it as the weekly checkpoint for the skill the labs build: not “did the code run” but did you interview well, direct clearly, and verify honestly — and, this week, can you see that your model actually worked on the images.

How it runs

• Presenters are drawn at random. Each week we pick 7–10 students live. Everyone must arrive ready — there is no volunteering-only and no opting out.
• 7 minutes to present + 3 minutes of discussion, per person. Keep to time; we will.
• You present by screen-sharing your viewer.html — the gallery, an overlay or two, and the metrics panel — and walk the room through what it shows.
• The rest of the room (and the teaching team) asks questions. Being able to answer them is the exam.

Being drawn with nothing prepared is a fail for that seminar. The random draw is the whole point: it means everyone spends Thursday thinking critically about their own work, not just the volunteers.

What to present — four things

You have 7 minutes. Don’t narrate the whole afternoon; make these four points land, using your viewer as the visual.

1. The problem — the question behind the question. What did the image data owner actually want? What decision changes when they know the answer? Show that you found the real question (segment what, count what, classify which classes) — not the vague one they opened with.
2. What you built. How you translated the interview into a brief (AGENTS.md / spec.md) and directed the analyst agent — which pretrained model (Cellpose, a CNN feature extractor, thresholding…) and why. The shape of the pipeline, not every command.
3. A critical read of your own method — show it in the viewer. Open an overlay: does the segmentation actually sit on the cells? Show your metric against its baseline. Which controls did you run (held-out split, class-balance check, a trivial baseline)? And, crucially, what did you refuse to claim?
4. The imaging caveat. Name the one image-specific trap you identified — pixel size / magnification, staining or illumination variation, class imbalance — and how it could bias the result. This replaces last week’s “what the literature says” as the point the room will push on hardest.

The single best thing you can say in a DDLS seminar is “here is the overlay, here is the metric that beats the baseline, and here is the imaging artefact that means I would not yet claim X.” That is what we are listening for.

How you’re assessed

Seminars are graded pass/fail on preparation and critical engagement — not on getting a “good” result. A modest finding, honestly interrogated and clearly shown, passes easily. A polished number with no overlay, no baseline and no caveat does not.

We are specifically listening for:

• Did you find the question behind the question?
• Where did you refuse what the agent handed you?
• What did you check — the overlay, the baseline, the caveat — and what did you take on faith?

For Master’s students, the course grade (A–F) comes from the final oral defence, not the weekly seminars — but the seminars are where you rehearse exactly that skill. Treat every Friday as a low-stakes run at the exam.

Attendance

Labs and seminars are the mandatory, live core of the course. You may miss one mandatory session in total — a lab or a seminar, not one of each. If you must miss the seminar, email ddls-course@scilifelab.se before the session, not after.

Attending and submitting are separate — the hand-in is always required. Even if you can’t join the live seminar, you must still upload your viewer.html (with your lab work) through the Hand in button in the course portal before the deadline: Friday 10:00 CEST, before the seminar starts. Missing the session (with notice) is excused; a missing submission is not.

How to prepare (Thursday, ~30–45 minutes — NOT in the lab window)

Do this on Thursday, after the lab — not squeezed into Wednesday’s four hours. This is the deliberate fix for last week’s “too intense” feedback: the 13:00–17:00 lab is for the interview, the analysis and building the viewer; seminar prep is a separate, later job. You already did the work in the lab, so preparing to defend it is quick:

• Open your viewer.html and decide the two or three views you’ll show live: the gallery, one good overlay, and the metrics panel. Know how to get to each in a few clicks — practise the screen-share once so you’re not hunting for the tab on Friday.
• Pull your artefacts from the lab if you need them: the interview transcript (Agent A), the analysis transcript (Agent B / Pi, saved as .jsonl under ~/.pi/agent/sessions/), and your AGENTS.md / spec.md.
• Draft a few slides or just present from the viewer. Slides are optional this week — the viewer is your main visual. If you want slides around the four points above, your agent can draft them from your summary; then fix them.
• Rehearse the 7 minutes once, out loud. If you run long, cut the “what I built” detail first — the problem, the overlay and the caveat matter most.
• Have one concrete answer ready for the discussion: if someone asks “how do you know the segmentation is right?”, you should be able to click straight to the overlay and the baseline.

You hand in the seminar via the portal’s Seminar card. This week you may submit your self-contained viewer.html as your deck (or a separate slides.html if you built one) — one self-contained HTML file, everything inlined, so it opens straight from a browser with no other files. We may pull it up on screen and present from your file, so keep it self-contained. Everyone submits, since presenters are drawn at random. Deadline: Friday 10:00 CEST, before the seminar — a live countdown is shown on the page.

This week’s lab sets up everything you’ll present. If you haven’t done it yet, start there:

• Go to Computer Lab 2