NCMIR - quick start guide for student interns

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NOTE: This page is a daughter page of: NCMIR

This page represents a set of guidelines I typed up in 2011 for new student interns at NCMIR, my old research lab, at the University of California, San Diego (UCSD). I left NCMIR in 2012, but wanted to keep this as permanent record of the guidelines I typed up. This page is currently restricted, but I may make it public later in case other people like the way I've written guidelines for interns to help them get oriented. See also: CellUniverse - guidelines for new members.

  • NOTE: This page is a duplicate of a restricted access page I typed up here

This page represents a guide for students thinking about doing an internship at NCMIR. It includes an important list of steps interns must complete before arrival, and also helps them know what to expect. It is recommended that all prospective NCMIR students should be shown this document at least two weeks before their work experience commences so they have time to complete paperwork.


The National Center for Microscopy and Imaging Research (NCMIR) is a 3D imaging and analysis laboratory which uses state-of-the-art microscope system to to help biomedical researchers understand biological structure and function relationships in cells and tissues. While the institute's main focus is on neurobiology, we also conducts research that addresses the cellular and molecular underpinnings of biological systems relevant to cancer, diabetes, and heart disease (to name just a few)! As a well known laboratory NCMIR attracts dozens of intern students every year, and hopefully you are one of them. Interning at NCMIR will not only give you great insight into real world cell biology and electron microscope facility, but also look great on your resume. If you decide to work here, the following document should help you (a) complete the preparation steps necessary before starting your internship, (b) complete required training, and (c) get started with working here.

Steps to Complete Before Arriving

If you read this page, you have probably already made e-mail contact with a scientist who's willing to take you on as a student intern. This person is your "supervisor". Your supervisor is the person responsible for assigning you work and (assuming you do a good job) writing you a reference letter after you're done. We highly recommend you ask for (and write down) their mobile in case you ever get lost, have an urgent issue or can't find them the day you arrive!

Before commence your internship, your supervisor will (hopefully) refer you to our (lovely) main administration lady Jennifer Santos (jsantos AT who will explain what forms you'll need to complete before arriving. If you are under eighteen you will need to get a signed letter from your parents (get template), which should be delivered in person or via e-mail attachment at LEAST a week before you arrive. Jennifer can also help you with many other issues, such as getting you scheduled for the required safety training - so make sure you e-mail Jennifer as soon as possible, and visit her office (halfway down the main corridor) on the day you start (if not before). Before you start Jennifer also will require you to e-mail her (and your supervisor) a "work schedule" where you state what days during the week you'll come in and out (a rough indication so she can keep track of you) and, most importantly, your start and end date for the internship.

In addition to completing written forms, there is an online form you must submit to request an "account". Go to Request a CRBS Single Sign-On (SSO) Account, and submit your details as per this example:

  • Name:                          Mr Joe Bloggs (your name here)
  • Requested Username:   jbloggs (best to follow this convention)
  • Email Address:    (personal e-mail will do)
  • Email address of CRBS Sponsor: (your supervisors e-mail address)
  • Reason for Request:     I'm doing an student internship for Dr Jane Plain, and need to be able to login to shared access computers.
  • SSH Key:                    NCMIR only      (here you'll probably just want to tick NCMIR and nothing else)
  • Resources you need to access:  blank  (leave blank unless you're a programmer - if unsure ask your supervisor)
  • Phone: - (can leave blank or enter your mobile if comfortable with that)

This online form tells system administration give you a login so you'll be able to login to most of our computers. Finally, make sure you know (as best as possible) what job you'll be doing when you get here. As a lab that collects a lot of electron microscopy images, the majority of our interns are put to work on "image segmentation" (tracing sub-cellular compartments). If your job is segmentation be sure to ask what dataset you'll be working on and where's it's located on the "Cell Centered Database"! If the dataset has not yet been moved to the Cell Centered Database your supervisor should do this for you, because without that done it's much harder for our group to keep a track of your work, and we'd hate to lose it! (Supervisors should refer to "" for instructions on archiving old data).

To summarize here is a checklist to tick off:

Checklist of Things to do Before Arriving:

  • (__) Contact NCMIR.
  • (__) Get yourself a supervisor.
  • (__) Get your supervisor's mobile number.
  • (__) Contact Jennifer Santos (jsantos AT and fill in internship forms and parent permission letter one week prior to starting. (MOST IMPORTANT!!)
  • (__) Give Jennifer a work schedule (including start and end date).
  • (__) Request a CRBS Single Sign-On (SSO) Account so you can log onto computer.
  • (__) Work out what job you'll be doing!

Room Access and Location

The main NCMIR lab (where you'll most likely be working) is in the Biomedical Sciences Building (BSB) at the University of California, San Diego (UCSD). For a printable map of how to get here see: NCMIR map. Our lab is located in "room 1000" (more of a huge lab space than a room), which is the wooden door immediately on the left after you go through the automatic glass doors at main west entrance into the building google map. After you walk through these wooden doors, you can find Jennifer Santos and the main admin office halfway down the corridor (about 100 feet) on the left, and labelled "Administration". If you get lost you can hopefully call your supervisor's number, or the the NCMIR's number (8five8)534-0276 or (better yet) just ask someone for help. Be warned that room 1000 is only unlocked between 8:00am-5:15pm - after that it will lock you out (even when you step outside to go to the restrooms) unless you've asked for the code. The glass doors are locked after 7pm weekdays and all weekend, so you'll only be able to get past this if you ask for a side key or swipe card from office administration, and these are rarely given to short term workers.

Safety Training

By USCD law we are required to give lab safety training to all new student interns. Only so many of these labs can be run, so make sure you contact Jennifer Santos early or it may not be possible to get you training and we won't be able to accept you. Safety training involves a relatively quick (<30 minutes) NCMIR lab safety tour, where we'll point out all the exits and danger zone, and also a much longer UCSD general safety course general safety course given by Mason Mackey which is relatively long (2-4 hours) including a PowerPoint presentation. It sounds like a lot, but the scientists here have to go through even more of these, so consider yourself lucky!

Work Ethic and Rewards

The reward for working at NCMIR is the chance to see a science lab (something for your resume), but if you do a good job you can also expect a reference letter from your supervisor and/or the director of NCMIR. These reference letters aren't just given away to anyone though! Your supervisor will set your working hours and you'll be expected to be fairly punctual and professional. We won't work you too hard or long, but at the same time we'd like to give you a feel for real working hours. You will also be expected to show your progress on your assigned task to your supervisor at least once a week... and most of our interns work for several weeks. In this lab we are appreciative of people who do good work, who demonstrate initiative and demonstrate good work ethic (i.e. not spending your day on Facebook).

Finding a Workstation

Intern students are typically placed in the area at the front of room 1000 where there's a bank of shared access computers in front of the whiteboard. Using the login you obtain you should be able to login to gain access to your internet/e-mail and (more importantly) have access to any software and data you need to work on. In the middle of summer, this main shared access area can get a little crowded, so you may not always be on the same computer. There are also many senior scientists near this area so please be respectful of nearby scientists and keep chatter to a minimum! If computers run out there is also a bank of computers in the "U-bend" shaped area, and if you need help there's a group of young (good looking) scientists in the opposite bank of computers who may be able to help you.

If you have any more serious issues, ask your supervisor to write a help ticket using our "Jira ticketing" system.

Segmenting Datasets

As mentioned, most interns are given work on "segmentation" (aka "tracing") projects. For these students you should refer and print out this page: Guide to Segmenting at NCMIR .


Interning at NCMIR can be a very rewarding experience, but to get the most out of it you'll have to be quite diligent! In particular, make sure you contact NCMIR early and stay in close touch with your supervisor to make sure you've ticked all the right boxes to make you ready to start. Once started we hope you enjoy your stay with us and learn some of the biology as you go.