I'm a first year PhD student in cognitive neuroscience, and I've been working/studying in this institution since my last year of master's degree.

My PhD project is the extension of my master's thesis project, which involves the use of rodents, and extra-cellular invasive recordings. Since the start of the PhD, I've been experiencing high anxiety and intrusive thoughts, for which I decided to start therapy. I recognize that my preoccupations revolve around my lab animals. My lab usually performs long experiments, with animals performing behavioral training protocols for extended periods of time.

Of course, rodents are living beings, and not everything can be under my control. This is something that I stress about, a lot. An animal might decide to slightly tilt the head in performing the task, and this can be very hard, sometimes impossible to correct: in this situation, one cannot record neuronal activity, for a number of reasons.

I'm in this situation, and not obtaining neuronal data means delaying my progress, which will be evaluated next year by the faculty, as it happens every year. This in turn makes me spiral so bad into anxiety and anguish. I'm afraid of the judgment of other people in the lab, especially those that are academically older than me.

I know I'm not the first student in a similar situation, and I'm aware that many feel the same as me. Plus, imposter syndrome is hitting hard, sometimes.

I'm asking for advice.

  • Have you ever been in a similar situation?
  • How did you manage to de-compress and cope with stress over situations that can't be 100% under your control?
  • How did you overcome fear of judgment, and fear of not being good/smart/capable enough?

I must admit that I have a positive relationship with my PI, and other lab mates, and that the majority of my problems don't have a very objective, precise, external cause, but they are impacting my quality of academic life. I feel overwhelmed and tired, and feel guilty if working less than my usual (8-5 or 8-4, mon-fri).

If this question is inappropriate, I apologize in advance.

  • 10
    There are many variants on an adage about ephys experiments that goes something like "You only need a month of experiments, but that month take 5 years to collect". Anyone who isn't having trouble is probably collecting junk data or fraud. If your paradigm isn't working, it's worth considering alternatives. Head-fixed experiments are popular for a reason and there is way more equipment available to assist now than 10-15 years ago.
    – Bryan Krause
    Commented Jul 13, 2023 at 15:19
  • Thanks for your kind comment. Unfortunately, head-fixed is not an option for me, for many reasons. This head tilt was corrected, then I had to move the animal to another apparatus (identical to the first), but the issue came back. If I solved it back then, probably I can solve it again. It's just that sometimes I feel so stuck and discouraged. But I still have a couple of months to solve the issue.
    – Acherontia
    Commented Jul 13, 2023 at 15:28
  • 7
    Beware of sunk costs and remember what your actual research questions are. Rodents tilt their heads.
    – Bryan Krause
    Commented Jul 13, 2023 at 15:37
  • 2
    Am I the only one thinking "if your research project depends on live animals being somehow made to hold their heads in unnatural and uncomfortable positions for extended periods, then don't do that research project"? Commented Jul 13, 2023 at 19:01
  • 1
    It's not an unnatural and uncomfortable position. Rats have to poke their nose in a nosepoking enclosure, and receive a vibration on the whiskers, and then turn left or right out of the nosepoke to receive reward based on their answers. They usually keep their heads straight, and when they begin to learn this task, they learn it with heads straight. Some of them tilt it slightly after months, which is not a problem per se. But with a chronic implant, tilting too much can result in damage of the implant, due to bumping against the nosepoke.
    – Acherontia
    Commented Jul 13, 2023 at 20:16

4 Answers 4


Yes! I've been there too. My PhD and postdoc both involved neurophysiology in awake, behaving animals. It can be very stressful to have your "progress" depend on something that's largely out of your control.

There are a couple of things to keep in mind:

  • Your supervisor has probably done similar experiments! They should therefore have reasonable idea about how quickly and consistently anyone can collect data. If not, consider adding a neurophysiologist to your committee so they can help set expectations; this might be especially helpful if other committee members come from more fast-moving fields. One of mine did human behavior and fMRI and it was very helpful to have another committee member remind him that animal training alone could take over a year.

  • Ask for feedback on your progress. Directly ask your PI "Am I doing okay?" Since you have a good relationship, I would expect a fair appraisal, but people do tend to forget how difficult things are and some may never be happy with any amount of work. Consequently, you may also want to look at published work as well. My PhD advisor insisted that he recorded 7 days a week and got publishable data almost every time. Looking at his papers revealed that was....not even close and that I was indeed working as hard, if not harder, than he had.

  • Adjust the experiment The two ways these projects go wrong is to either a) constantly change everything or b) never change anything. Instead, deliberately consider deliberate changes that can improve your odds of success. The problem you describe in the comments sounds like it could be fixed with some engineering: carve a hole in the nose poke apparatus so the implant has more clearance, add some material elsewhere to better constrain the approach/exit angle, or beef up the implant so it's less likely to be damaged. If your institution has a friendly machinist or veterinarian, ask them for advice. Think about changing the task too. Your scientific question can probably be answered in many different ways. Could you (for example), put a lickometer in the nosepoke, so that the animal doesn't need to move? Or perhaps you could explicitly train them not to press against the implant (e.g., by adding a timeout). Discuss any ideas you have with your lab/committee. Not only will the feedback be useful, but it should demonstrate that you're thinking hard about your research.

  • Adjust your PhD. The stress presumably comes from feeling like these experiments are make-or-break for your PhD, so giving yourself some other/backup options can really help. Could you do some human psychophysics or computational modeling related to your experiment? Analyze some existing data? Write a review? I would consider trying to do (say) four experiments a week and spend Fridays on a side project that's more "deterministic".

  • Realize how you're being evaluated. A few people may judge you strictly on your ability to produce data and it's obviously part of being a scientist. However, most people——and especially the good ones——will also consider your effort, attitude, and intellectual approach as well. For what it's worth, I would be impressed if I saw someone at their rig, day after day, working hard and intelligently. This impression would only slighly be affected by their yield, especially for a grad student. If they were moving slowly, I'm more likely to think that the project is tough or that they should be getting more help.

  • Don't compare yourself to others. Ephys is slow and difficult, as is animal behavior, and the combination is infamously worse. Most of the broader field of neuroscience knows this, so don't feel inferior to a classmate doing (e.g.,) MTurk experiments or modeling, where they can quickly bang out papers. Your reference letter-writers should also be able to explain this fact.


You are not alone.

Your title question How to manage stress during a PhD, when your research project involves working with lab animals? was addressed in a recent Science March 2023 article, "Suffering in Silence: Caring for research animals can take a severe mental toll. Is anyone listening?".

The article appears to be free so I encourage you to read it. Some key points from the article:

  • Support groups exist for people who work with animals
  • You're not alone
  • Tools exist to reduce stress for students and animal care givers in academia

Not an experimentalist, so take from this what you will.

The first question that comes to mind is are you anxious because you're doing experiments on animals (which may feel unethical to you) or are you anxious because you can't control every aspect of the animal when doing the experiment?

If the first case then maybe another aspect of research may be better for you.

If it's the second case (which it sounds like because you are talking about how tilting the head destroys your data) then you should maybe re-frame how you are thinking of this. You seem to be saying, an animal does this behaviour which stops me from taking (neuronal) data. Instead of thinking the animals could destroy my experiment at any time, start a second project focused on: what method could I use to be robust to this animal behaviour. This project itself may end up being more valuable than your original project if you develop a good method to account for head movement when trying to measure neuronal data, leading to a paper describing what might later be colloquially known as Acherontia's method.

Basically what is happening is you try to do some science, find something isn't as well understood or developed as you'd like it to be, and do some science on this alternative topic. Even if you never solve your original project, solving this new problem is science, one of the may incremental steps of it.

  • 1
    For me, the stress came from the fact that so many things can prevent you from taking data (and thus, advancing) but it's impossible to solve them all and many aren't even that interesting. For example, the head tilt issue seems like it might just be the rat smashing delicate gear against hard objects. It'd be good to fix it but a) you/your PI may not care or have the skillset b) it'll just be something else (immune response destroying the electrodes, animals aging or falling ill).
    – Matt
    Commented Jul 14, 2023 at 6:16

Have you ever been in a similar situation?

Oh yes. I've been doing research in neuroscience with rats for about 10 years now. In the first year of my PhD I ran 7 experiments lasting about 1 month each which basically all failed: the rats didn't seem to learn what I wanted them to learn. I was pretty stressed out by the end of that... but it lead to a re-thinking of my whole approach and scientific question, and my 8th (and last) PhD experiment was successful and is now published.

How did you manage to de-compress and cope with stress over situations that can't be 100% under your control?

Try to fix it, give up & move on if you can't fix it. Learning to give up is a big part of being a scientist. Also... no situation in biology is ever 100% under your control and I'm afraid you just have to accept that (other researchers in your field already know it, and will judge you accordingly). Lastly: make sure you have hobbies (especially which involve physical activity) to help you stop thinking about work.

Specifically, you say:

An animal might decide to slightly tilt the head in performing the task, and this can be very hard, sometimes impossible to correct: in this situation, one cannot record neuronal activity, for a number of reasons.

This seems like enough of a problem to need a fix. Spend some time figuring out how to improve this, ask your supervisor, if they don't know, ask other scientists that work with the same technique, try things out.

How did you overcome fear of judgment, and fear of not being good/smart/capable enough?

I wrote my PhD... until then I was definitely unsure of my abilities as a scientist. Reading papers and obviously publishing papers helps a lot, but the feeling of not knowing enough never goes away. I don't mind being judged anymore though: that's how you improve!

This in turn makes me spiral so bad into anxiety and anguish

This is worrying me a little bit.. is this a recurrent feeling or does it happen rarely? It is not normal to feel too anxious too often, even for a PhD student. The most prominent feeling should be enjoyment, curiosity, excitement... do you at least get some of that?

In conclusion: you cannot control everything, and your colleagues know this; but you should attempt to improve things that you have control on to maximize your chances of getting valid results. Good luck!

  • 2
    I'm coming a bit late to comment, but thank you! It seems like I managed to fix the head issue, and the project is going on, my PI is presenting some of my results at an important seminar, and I just sent the abstract for a poster presentation at a conference. As per the last point, I get somehow lost in my mind, and I'm taking psychotherapy sessions. Thank you for sharing your experience!
    – Acherontia
    Commented Sep 12, 2023 at 16:42
  • Glad to hear :)
    – user126108
    Commented Sep 14, 2023 at 0:25

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