In this episode we’re featuring remote access developments at the National Center for Electron Microscopy (NCEM), one of the characterization facilities at the Molecular Foundry. NCEM is home to cutting edge instrumentation, techniques and expertise required for exceptionally high resolution imaging, and analytical characterization of a broad array of materials.
Transcript:
Shannon Ciston
Welcome to this episode of Foundry from Home, a podcast to highlight new developments in remote, virtual, and physically distanced user access to the Molecular Foundry. I’m Shannon Ciston, the User Program Director at the Foundry. Today, we’re featuring remote access developments at the National Center for Electron Microscopy, one of the characterization facilities at the Molecular Foundry. NCEM is home to cutting edge instrumentation, techniques and expertise required for exceptionally high resolution imaging, and analytical characterization of a broad array of materials. Our guests today are NCEM staff members, Dr. Karen Bustillo, principal scientific engineering associate, and Dr. Peter Ercius, staff scientist. Thanks for being here with us.
Today, our guests are going to highlight for us some of the innovations and user access to transmission electron microscopy at NCEM. Peter, let’s start with access to the TEAM 0.5, I understand that users are actually able to control the microscope from their home location. Can you tell us a bit more about that?
Peter Ercius
Yeah, thanks a lot for having me on. Actually, I’m very happy to talk about this. So the microscope that I’m in charge of called TEAM 0.5, is about 10 to 12 years old right now, and it is still using Windows XP. It’s amazing how fast technology has progressed over this time, but Windows XP is old now and can’t be on the internet anymore. So if we want to be able to control the microscope remotely, we had to come up with a different idea. So I’m collaborating with a user named Wolfgang Theis in the UK and we’ve created a server client model where we install a special server on the microscope that can press all the buttons and run scripts and do everything that we want. And then we connect remotely through a separate computer that we call the support PC, to a client that we developed also. So the client allows up to five people to be connected at once and they can fully control the microscope from their their home computer, basically with a laptop. So the client interface captures all the major functions of the microscope in one page. So you can change the magnification, you can center the stage, you can change the focus, you can do more complex experiments, like taking a focal series. All kinds of things – anything that we can think of that we want to do with the microscope, we can pretty much script. It can also run in an automated fashion where it takes data for you, when you’re not even there. And all the data, every image that you take, is saved in one place and it’s easily browsable by all the team members. So if one person presses a button on their client, it acquires the data and sends the data to all the clients that are currently connected so everybody can see all the data that comes in all at the same time.
Shannon Ciston
Very nice. And so do you have users working on the same project that are in different locations?
Peter Ercius
Yes, so the earth, you know, turns and some people are up and other people are asleep at times. So we actually have an international team working on a project together. So I’m here in the US and I can operate the microscope while I’m awake. And then we have a team member in the UK who can operate while we’re asleep. And we have another team member who’s in Korea who can operate the microscope while the rest of us are asleep. But at least two people are usually either working on or talking about the microscope at the same time. So that works really, really well. But the only problem then is coordinating all this between three team members who are now in disparate locations, right. So we’ve been using these collaborative chat programs such as Google Chat, or Slack and we find these extremely useful. Everybody can type into the chat as the experiment goes on. And if something happens, or if there’s a problem, we can alert somebody or we can ask for help. It also creates a play by play of what’s happening during the experiment. People can upload cell phone images of what they see, we can upload screenshots that are taken from the client, we can upload data, we can upload metadata, we can keep track of when some setting on the microscope was changed, and then everybody has that. Email is not really good for this because if somebody doesn’t reply all and then everything gets all messed up. So these chat programs are really great. The other thing is that all the data is acquired in one file, and it’s all stored in a shared drive. So the data is automatically available to everybody in the team all at the same time. So this, not only the chat, but also the the file itself creates kind of a real time lab notebook, which captures all of this digital information that is very difficult for you to write down in one lab notebook that only one person would have access to. Otherwise, you’d have to scan it and send it around. And that’s just not going to work out. So while we’re talking about the experiment, and doing the experiment, we can have somebody else doing the analysis because they have access to the data immediately. Also, you can even be talking about writing the paper at the same time as you’re doing the experiment. So this has really worked very well. And I think it’s, it’s actually going to change the way that we work going forward in the future.
Shannon Ciston
That’s great. Thanks, Peter. And Karen, what about for other teams at NCEM? I understand you’ve been able to support collaborative team sessions as well, can you tell us what that looks like during the experiment?
Karen Bustillo
Sure, so we rely heavily on zoom and the ability to screen share multiple screens at the same time. So the same software that Peter talked about, the virtual network computing or VNC software, we use that to access these computers that aren’t on the internet. But instead of driving the microscope remote remotely like Peter talked about, we just share that screen on the zoom meeting. And that enables the users that are on this zoom meeting to see the microscope controls, we might also share a second screen with a camera or a third with some analysis software, maybe even an optical microscope. And this allows everybody on the zoom meeting to see what’s going on. So one of the benefits of these day long zoom meetings is that multiple people are working collaboratively, and then data collection becomes really efficient. It’s always a good idea to have the person who made the sample on the call. And we were even doing this before the pandemic using Skype so that the person who makes the sample can provide insight about the material. One person is usually usually charged with taking notes in a shared document. This is usually a Google Sheet that’s shared on a drive and this standardizes the file names and experimental parameters, just like Peter talked about. So at the end of the day, you have this Google Sheet, which is like a cheat sheet for all this saved data. Another collaborator might be tasked with transferring the data live and doing some analysis to provide feedback, usually within the hour about how the experiment is going. And faculty advisors and undergraduate students sometimes jump on during the session. This is really exciting, it’s brand new, that they can just pop in and see what’s going on, they can ask questions, it’s a great way for new users to actually see what’s going on without actually being in the room. And then during the data acquisition, there’s often some dead time while we’re acquiring data, and we can talk about what’s going on, talk about the data we’re collecting, talk about the next steps, and ask questions. So I think the pandemic has forced us to be more intentional about the experiments we’re doing, and to be more inclusive during the session. And this results in organized data at the end of the day and a plan for the next steps.
Shannon Ciston
That’s great. So it sounds like in this mode, typically you have the user working at the microscope, and then the staff staff member supporting from a distance. But you also work the other way around sometimes right with the staff local and the user remote.
Karen Bustillo
Right. So for users that don’t live locally or cannot travel at this time, sometimes the NCEM staff will drive in the microscope while the users are on the zoom meeting. So they ship samples to NCEM and they’ve been pre-checked and we’ve talked about the plans for the experiment. The Google Sheet is all set up and the users are on the zoom meeting the whole time, along with hopefully a third person who’s doing analysis at the same time.
Shannon Ciston
Thanks. So that sounds that sounds like it’s really enabling a lot for for that collaborative work. That’s exciting. And I think you mentioned that NCEM also using tools like zoom to support user training. Can you tell us you know which instruments or capabilities that training applies to?
Karen Bustillo
Right, I think most of the microscopes are set up for remote training right now and some staff are definitely actively training. So we use the technology we have, as I mentioned, a lot of extra computers so we can screen share. We all have webcams that are set up on tripods, high quality microphones, extra speakers. There’s a landline phone in each room – we’re trying to discourage users from using their personal devices to protect them from being contaminated by the shared surfaces. Most users come to NCEM with a working knowledge of TEM so we have this shared vocabulary. So ideally, all the training can be done via zoom meeting either using words or sometimes we use the Zoom whiteboard. But in some cases a concept needs to be conveyed. I’ve made short movies that I can quickly share with the user to explain a concept. And sometimes I even run downstairs and open the door, while I stand in the hallway and point with a laser pointer. So we’re trying to use every resource we have to make this work.
Shannon Ciston
Sure. That’s great, and Peter, I heard that users are able to do some of the data analysis remotely as well, can you tell us briefly which types of analysis people can access remotely?
Peter Ercius
For sure. Right now, data analysis and TEM is one of the most important things that you need to do, and a lot of people get a lot of data. But there’s a lot of advanced experiments that you need to do a lot of data analysis, sometimes on very huge data sets, after you take all this data. So we used to have a computer lab, well we still have a computer lab, but people can’t really go in and use it and not many people can be in the same computer lab room at the same time due to COVID restrictions. So what we’ve enabled is remote access to those computers in our computer lab that has this specialized software, sometimes proprietary software that’s expensive, which we purchase for users to use, in order to do some of these very complex experiments, and access some of the data that they acquire. So that remote login is working quite well, just using VNC, or remote desktop, which is great. But the other thing that’s happening a lot is, if you have really big data sets, sometimes people’s own laptops, or even a very advanced computer that they’d buy at home wouldn’t be able to analyze something. So we’re starting to work more with supercomputers like NERSC or the Molecular Foundry cluster itself. But all the data is on the supercomputer, and all the analysis software is on the supercomputer and you can access everything remotely, so there’s no need to be there anymore.
Shannon Ciston
All right. And that’s all we have time for in this episode. I want to say thanks so much, Karen and Peter, thank you for sharing with us about these innovations at NCEM. And it’s really, yeah, it’s really exciting to think about what what these are gonna do for enabling user access. So we appreciate all your work toward that end. Thanks for listening everyone. Please look for more episodes of foundry from home as we continue to highlight developments in virtual remote and distance user training and access throughout the molecular foundry.
This has been a production of the Molecular Foundry’s User Program Office and communications team. The music used in this production was “Still room on the night train” by Ketsa courtesy of the Free Music Archive.
The Molecular Foundry is a US Department of Energy Office of Science user facility at Lawrence Berkeley National Laboratory.
Transcribed by https://otter.ai
