Final Lab Report¶

NEU466G, Dr. Harris · Class documents

Overview¶

The final lab report is worth 100 points. You submit a draft for peer review in Week 14, review a classmate's draft in class, and submit the final report on Canvas by 11:59 PM on the Sunday after the Week 14 class. See Assignments for the peer review.

Submit one PDF with Figures 1 to 5 and Table 1 inside it. Submit the supplemental tables as separate files. Put the final word count in parentheses after each section header.

Grading is stricter on the final report than on the earlier drafts. Read the tips at the end of this page before you write.

I. Report sections (62 points)¶

Section	Points	Max words	What it must include
Title	1	20	Reflects the topic and the main conclusions. Put your name and your undergraduate department under the title.
Abstract	4	150	Open with the rationale and goals. Briefly state the main features of the methods and results. End with your main conclusion about how 3DEM could add to what we know about your Discussion topic (for example, synaptic connectivity in a brain region for hearing, speech, or sleep; inhibitory synapses in epilepsy; or disruption of recycling pathways in Alzheimer's disease).
Introduction	5	250	Synaptic research using 3DEM. Cite at least five papers (from the class readings or the literature) that introduce the objects you analyzed. End with a statement of what 3DEM is and why it was needed to study the structures in this class.
Methods	10	250	Summarize the methods: animal source, brain region, tissue preparation, and imaging method. Describe how you used PyReconstruct for 3DEM data collection.
Results	20	1,000	2 points: a subheading for each of the 7 sections (Figures 1 to 4, and the 3 parts of Figure 5: autosegmentation, nascent zones, perisynaptic glia). 18 points: in each paragraph, open with a topic sentence, describe the figure or figures, and include statements about your experience reconstructing the object (for example, "The nascent zones for 5 of the spines were difficult to identify because the PSDs were too oblique," or "4 of the spines were merged because..."). End with a statement of your conclusions or outcomes.
Discussion	20	250 (500 for graduate students)	Read and combine the results of 5 papers (10 for graduate students) on your topic of interest: more than 3 primary papers (6 for graduate students) and fewer than 2 reviews (4 for graduate students). Summarize what ultrastructural analyses have shown so far. Then, from your experience in this lab, discuss how 3DEM and connectomics could give new insight into your topic.
Bibliography	2	None	List every cited reference in 7th edition APA format, including the DOI. Include the references cited in the Introduction and the Discussion.

II. Figures 1 to 5 and Table 1 (27 points)¶

Give the word count in parentheses at the end of each legend. See Figure Legend Example and Tips.

Item	Points	Legend max words	What it must include
Figure 1	4	150	Excitatory synapses: postsynaptic structure. Follow the figure rubric and the draft feedback. Include a title, a description of each panel in order, and the arrows and colors that identify structures. Show the graph as the rubric says. Include scales.
Figure 2	4	140	Excitatory synapses: subcellular resources. Same requirements as Figure 1.
Figure 3	4	175	Excitatory synapses: presynaptic components. Same requirements as Figure 1.
Figure 4	4	175	Inhibitory synapses. Same requirements as Figure 1.
Figure 5	6	200	Autosegmentation, nascent zones, and glia. Follow the figure rubric and the peer feedback. Include a descriptive title, a description of each panel in order, and the arrows and colors that identify structures. Include scales. See Figure 5 Instructions.
Table 1	5	100	A summary table with data that quantify the outcomes of autosegmentation, nascent zones, and perisynaptic astroglia. The word count includes the title and the abbreviation definitions, but not the table contents.

Table 1 summarizes these items:

Table 1 item to quantify	Value
C-trace volumes (range in cubic micrometers before proofreading)
C-trace volumes (range in cubic micrometers after proofreading)
% protrusions without synapses
% shaft synapses
% multisynaptic spines
% branched spines
% synapses with nascent zones
% synapses with perisynaptic astroglia at the ASI
Range in number of glycogen granules in perisynaptic astroglial processes

III. Supplemental tables (6 points)¶

Component	Points	Guidelines
Supplemental Table 1	3	Upload one Excel or PDF file titled "SuppTab1_EID" with all the data you used for Figures 1 to 4. Keep it well organized, with column headers for every variable used in Figures 1 to 4 and in your calculations.
Supplemental Table 2	3	Upload one Excel or PDF file titled "SuppTab2_EID" with all the data you used to make Table 1. Keep it well organized, with column headers for every variable entered by synapse number.

IV. Writing quality (3 points)¶

Sentence structure, grammar, spelling, and punctuation. Avoid run-on sentences and a vague "This": a "This" must be followed by a noun or phrase that says what it refers to. A spell checker or grammar checker can help you find problem areas.

V. Response to peer review (2 points)¶

In the Acknowledgements section at the end of the report, thank your peer reviewer and say what you changed in response to the review. Also thank your professor and TAs for their help and for preparing the EM series.

Tips for the final report¶

Explain how each object was identified, and what it does. More points come off if you do not. Avoid circular statements such as "Polyribosomes are identified as clusters of ribosomes" or "Synapses are identified by their PSDs." What do ribosomes look like? What do PSDs look like?
Say how you decided a synapse was inhibitory or excitatory. List 3 criteria.
Say why you looked at the nearest neighbor synapse when deciding whether a synapse is inhibitory. If this is unclear, ask your TAs.
Put the word count after each major heading, for example INTRODUCTION (### words) and RESULTS (### words). Do not put it on the subheadings and expect the grader to add them up.
Name the brain region correctly. The ZGBJY series is from the dentate gyrus, not CA1. The Week 2 lecture and Nam et al. (2025) also use the dentate gyrus.
Cite in the text. Make a statement and cite it in parentheses, for example "(Harris, 2025)."
Leave colors out of the Results. Colors belong in the figure legend. The Results is not a legend, so change your writing style for it.
Do not write "Fig 1 shows... Fig 2 shows... Fig 3 shows...." Make a scientific statement and follow it with the figure, for example "(Fig. 1A)."
Follow APA format in the bibliography, including the italics.