are you familiar with the allen brain atlas data portal http connectivity brain map org

Directions: This exam will require internet access to the Allen Mouse Brain Connectivity website:

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The exam is 10 questions long, with some questions having sub-sections. For some questions you will be asked to fill in the blank with the structure name and on some questions you may also be asked to justify your answer with a brief (2 sentences ONLY) response. All written responses must be as concise as possible. Responses longer than 2 sentences will not receive full credit.Each sub-question is equally weighted, so for example, if question X has 3 sub-questions and question Y has 1 sub-question, question X will be worth 3 points (3 sub-questions) and question Y will be worth 1 point (1 sub-question).

There are a total of 30 points possible on the exam. As stated in the class syllabus, this exam will be 15% of your total grade for the course.

For each question structures will be listed with their full name capitalized followed by their Allen Atlas abbreviation in brackets, with all text of a structure name underlined. For example, the “Main Olfactory Bulb [MOB]” refers to the structure commonly called the main olfactory bulb and abbreviated as MOB in the Allen Atlas search fields. Although not required for your answers, it may be helpful to keep track of the experiments from which you obtain your answers in case clarification is required afterwards. Make sure all of your answers are based off of the Allen Mouse Brain Connectivity Atlas and not outside sources.

The first questions will test your general knowledge about using the Allen Brain Atlas.

QUESTION 1: Provide 1 reason why you would choose one experiment over another when using the Allen Atlas.


QUESTION 2: From the images provided below, pick which injection target most likely came from anintegrative brain systemor sensory brain system. Explain your reasoning (4 pts).

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QUESTION 3: The red cross on the images marks the injection site of the two experiments. Based on your knowledge of external anatomy, which brain lobe seems to receive input from both of the injected structures. What sensory system does this imply both areas communicate information to?

  • 1.Lobe: ___________
  • 2.System:__________

Starting at the front of the brain, we will explore the connections of the Main Olfactory Bulb [MOB].

QUESTION 4:What are the 2 main areas the MOB send projections to?



QUESTION 5: Do these structures send projections back to the MOB? (Yes or No)



QUESTION 6: Find an example of a structure both of these areas (from Question 3) project to.


QUESTION 7: What structure receives the strongest input from the structure you just indicated in Question 6?


Next, we will explore a second sensory system, the visual system. We will start with the input to the brain, the axons coming from the Retina [retina].

QUESTION 8: Which structures receive the strongest input from the retina within two specific brain areas, the first in the Thalamus (TH) and the second in the Midbrain (MB)?



QUESTION 9: Do these 2 structures have reciprocal connections with one another? (Yes or No)


QUESTION 10: What is a common projection both of these structures have?


QUESTION 11: What is the strongest projection from each structure?



We will now move from sensory systems to structures associated with memory.

QUESTION 12: Which structure sends the most input (measured as Tgt Vol) to the CA1 Region of the Hippocampus [CA1]?


QUESTION 13: Where does this structure receive its strongest input from?


QUESTION 14: Which structure sends the most input (measured as Tgt Vol) to the Dentate Gyrus Region of the Hippocampus [DG]?


QUESTION 15: Where does this structure receive its strongest input from?


Finally, we will wrap up our brief tour of neural systems by looking at the motor output of the brain.

QUESTION 16: Which structure sends the most input (measured as Tgt Vol) to the Primary Motor Cortex [MOp]?


QUESTION 17: Where does this structure receive its strongest input from?


Now you will open two specific experiment from the Allen Atlas links and answer questions about the experiments.



QUESTION 18: Name the common injection site of the two experiments.


QUESTION 19: What is the main white matter fiber tract this area utilizes to send information?


QUESTION 20: Look for any differences in the projections shown across the two experiments and check the transgenic information for each experiment.

What are mouse lines used for each experiment?


QUESTION 21: Knowing that both experiments share a common injection site, could this difference in mouse lines be a reason we see differences in the projections? Explain your answer (2 pts).