KH LabClass Research Project: Overview¶
Overview¶
In Weeks 7 to 14 (Module 4) the class works as one research team on a real question that has not been answered yet. You work in a group. Each group reconstructs one dendrite from the dentate gyrus of the hippocampus, and the class puts the data from every group together to answer the question.
You use the skills from Modules 1 to 3: tracing and classifying synapses (Labs 1.1 and 1.2) and finding spine resources (Labs 3.1 and 3.2). The project pages are:
- Synapse categories (Weeks 7 and 8)
- Postsynaptic resources (Weeks 8 and 9)
- Data curation (Week 11)
- 3D analysis (Weeks 12 and 13)
The research question¶
To be decided
The class dataset is coming: where the dendrites come from, the conditions, the time points, and the question. Dr. Harris writes the background for the question and its final wording.
Groups and dendrites¶
- In Week 7 the class splits into project groups, and each group is assigned one dendrite. On these pages it is called your group's dendrite.
- The data are blind. You do not know which condition or time point your group's dendrite comes from until the class unblinds the data in Week 12. Blind data keep what you expect from changing what you see.
- You get the series file and its image folder for your group's dendrite from Canvas. Synapse categories says how to set them up.
To be decided
- How many students are in a group, and how groups are formed.
- How a group splits the work on its one dendrite (for example, by sections or by spines).
- What the series holds when you get it: only the dendrite shaft, or the spines and synapses already traced for you to check.
Week by week¶
| Week | Topic | What you do |
|---|---|---|
| 7 | Project introduction | Join your group, get your dendrite, and classify its synapses (Synapse categories). |
| 8 | Postsynaptic resources | Student-led paper discussion. "Look and see" synapse categories (Synapse categories). Start stamping resources (Postsynaptic resources). |
| 9 | Postsynaptic resources (continued) | Finish stamping the resources in every spine of your dendrite. |
| 10 | Class data | The class puts every group's data together, then discusses it (Class data). |
| 11 | Unbiased sampling and sources of variation | Check and clean the class data (Data curation). |
| 12 | 3D exploration of synapse density and clustering | 3D dendrite analysis in Blender (3D analysis). The data are unblinded. The final lab report rubric is handed out. |
| 13 | Class data and discussion | More Blender work. Each group gets its figure for the presentation. |
| 14 | Oral presentations | Each group presents. |
The schedule lists what is due each week.
Class data¶
In Week 10 the synapse categories and resource stamps from every group become one class data set. Each group's dendrite is one sample. The comparisons between conditions and time points use the whole class data set, not one group's dendrite.
To be decided
How the class data are collected (for example, one shared spreadsheet, or an export from each group's series) and what each group adds to it.
What you submit¶
- Every week: your saved series (.jser file), uploaded to Canvas before you leave class. This counts for attendance and data management.
- Week 8: the student-led paper discussion.
- Week 12: the curation lab report.
- Week 14: your group's oral presentation, and your own final lab report.
Assignments describes each one and its share of the grade.