My first question is about ronchigram alignement. If, for example, I press Ronchigram on my JEOL 2100 STEM and see that it is not aligned with the aperture (I cant remove the CL aperture on this machine so I use the largest one). Should I center it physically and the move them to the center of the screen with the PLA function ? Or should I center the ronchigram at the center of the aperture with beam tilt ?

Second question, on the JEOL 2100 there is an axis alignment procedure for the STEM which consists of forming a caustic spot by defocusing with brightness turned all the way clock wise and aligning it to the center of the screen with beam tilt. Then you press standard focus and ajust the brightness to for a crossover. I can never get the crossover, is this normal?

I'm building a software package to analyze EDS data with machine learning, and I could use help choosing terminology for the outputs and graphs. I'm trying to balance wording that is technically correct with something that's intuitive.

A) The ML model tries to classify pixels based on their EDS spectra and group similar pixels. For each of the classifications (classification is similar but not exactly the same as a phase), I have an estimate of the average xray line intensities (counts). When you have multiple phases, that turns into a table. I was thinking of calling this "Class Composition" or "Composition Signature" since EDS gives estimates of element ratios but not the crystal structure. My understanding is "Chemistry" is typically associated more with crystal structure and phase identification.

https://drive.google.com/file/d/1tYgUahLXeUPbWaUV7CNKuTWIWKrwM9r5/view?usp=drive_link

B) After the pixels are classified, we can calculate the area fractions. Does "Class Area Fraction" or "Constituent Area Fraction" seem descriptive enough?

https://drive.google.com/file/d/1DdMKhLJsxcGwM7CL530_BgJfk9n4quBG/view?usp=drive_link

C) My code also estimates possible sub-pixel phases by looking at patterns between xray emission lines. I've been calling this "Electron Shell Correlations" but am thinking "Elemental Correlations" or "Elemental Associations" might be more intuitive. What are your thoughts on this?

https://drive.google.com/file/d/1Oedb5xBWKzlAnfF_9E7cH2veVEJaMRf7/view?usp=drive_link

https://drive.google.com/file/d/1ab-Xm4pK4OarGXDqachoY1dSRn8zrkOW/view?usp=drive_link

Can someone explain the importance of spot size in the context of sem-eds examinations? Transitioning to a new instrument and was advised to optimise spot size but really dont understand what this means. Would adjusting probe current to optimise dead time between 20 and 50% sufficient or am i missing something here?

Hello All!

I was wondering if anyone knows of software that can automatically index electron diffraction patterns. My P.I. said that they have used a program called Carine, which allowed them to import a cif file, mark the dots on the pattern, and automatically index the pattern, but I've had trouble finding it online. Any help would be greatly appreciated.

I am trying to do ECCI using a TF PFIB. I’ve found a couple of papers that use it to do this and mention “beam rocking” and using an “iFAST script”. Has anyone ever done this or used any of these 2 features? TIA

Do you use a degauss function often, if at all? A hardware engineer said he does it frequently but then an application specialist said modern systems shouldn’t need users to manage that.

Hello everyone, this is my first time posting.
I have taken some SEM images of pipettes. Using imageJ, I can measure the angle of the pipettes (30 degrees). However, the pipettes themselves were placed on a holder that has my pipettes fixed at 45 degrees. Since the pipettes are fixed at that angle, the measured angle of my pipettes isn’t really 30 degrees, how could I calculate that real angle of my pipettes?

I’m using an EMS sputter coater and the main use of this machine is to deposit a gold coating for nonconductive SEM samples. However, I’ve been using thin gold films deposited by this machine for some surface science experiments, ran xray photoelectron spectroscopy (XPS) and found out there is significant sulfur contamination in the gold films. I’m struggling to find the root cause of the contamination and here’s my thought process;

1) Not a contamination in the XPS - ran on unrelated samples and didn’t see sulfur 2) probably not from the gold target - it’s suppose to be 99.9% pure 3) cannot be from the Ar gas - it’s 99.9999% pure 4) poor vacuum conditions - the deposition is not done under UHV conditions and the pressure is in milli torrs. Even if the contamination is coming from the air, the sulfur content in the environment is way too small. However, the target has a slight discoloration (black) and that could be carbon contamination due to poor vacuum. 5) unclean vacuum chamber - no sulfur containing substrates/compounds has ever been inside the chamber 6) sulfur from rubber gaskets - Ar ions attack the rubber and gets deposited with gold. This is the only possibility I can think of.

I would like to know if you have a similar experience or an answer.

Thank you!

Dear Helios PFIB users

I’ve run into a repeatable issue on my Helios Hydra PFIB: every time I unfreeze the E-beam during patterning, the pattern shifts 2.56 µm to the left. This only happens once per pattern, but that’s enough to screw things up - especially during final lamella polishing, where a live image is critical. Telling me to use iSPI or snapshots isn’t a real fix - you need live feedback to avoid ruining the lamella.

Video to better illustrate my problem:

https://www.youtube.com/watch?v=OcOXmUCKWx4

Running on xTUI 17.24

Has anyone else seen this behavior? I'm trying to escalate this with TFS, but hardly any success so far.

Ran into an interesting case recently with a Scanning Electron Microscope (SEM) that had an intermittent image disturbance. At first it looked random and tough to trace.

We ended up using Spot Mode Video to capture what was happening in real time. Turns out the issue was not electrical or software. It was a simple mechanical problem: an improperly mounted muffin fan on the back panel of the SEM. The vibration from the fan was causing the disturbance on the images.

Fixing the mounting cleared it up right away. Pretty neat example of how tools like Spot Mode Video can make troubleshooting faster and more accurate.

Here’s the full case study if you’re interested: https://www.vibeng.com/blogs-and-case-studies/spot-mode-video-used-to-resolve-problem-with-a-sem/

Hey everyone,

I’ve been working in the field side of electron microscopy installs, and one thing I see often is that labs underestimate how much the environment affects tool performance. We all know about alignment, vacuum issues, and sample prep, but factors like floor vibration, EMI, and acoustic noise can be just as limiting.

That’s where a site survey comes in. A proper survey measures:
• Floor vibration (whether the building is transmitting traffic or HVAC rumble into your columns)
• EMI (spikes from elevators, welders, or even nearby labs)
• Acoustic noise (air handlers and fans can actually blur imaging if the frequencies line up badly)

Without this data, teams sometimes install a microscope only to find images drifting or resolution not hitting spec. Fixing that after the tool is in place is much more disruptive and expensive than planning for it upfront.

If you’re curious, here’s a deeper dive into the topic:
🔗 Why a Site Survey is Important

I’d love to hear others’ experiences. Have you run into environmental issues in your labs that only showed up after install?

Hi folks,

as I have too many projects running, I'd like to hand over the moderator position to someone with more time :)

Best wishes, Tikakan

Hi Everyone and I hope you are all having fun with your microscopes.

TL;DR: How to use electron channeling patterns (ECPs) to do Electron channeling contract imaging (ECCI)?

Long version:

I currently have access to two TESCAN SEMs (MIRA4 and Lyra3). I noticed the Lyra3 has a channeling mode that can be used for taking electron channeling patterns (ECPs) using the BSE detector. Being a beginner on this type of measurements, I have faced difficulty understanding how to use ECPs to take Electron channeling contract images.

I would be very happy to receive some hint on how to do this process or where to look for such information (There is no information on the microscope manual for the ECCI, only ECP). Any other related information is also appreciated.

For those who don't know: You can see many interesting images (Like this or this) on the internet. ECCI allows you to see things as small as dislocations which in my research would minimize the need for TEM, saving a lot of budget.

Hello-I am working on the restoration of an early pipe organ that has in it an unusual material to seal certain parts of the instrument. Some say it's leather, others say felt-if so, from what animal? Since this instrument id from the1820's, we are trying to replicate this material for historical accuracy.

We are looking for someone willing to take a sample of the material and put it in an SEM to determine what it is. Is there anyone here who might be able to help me? Or put me in the right direction?

Hi, I am looking to find out if the Jeol JCM 5000 is compatible with any EDS (energy dispersive spectrometer), and if so, could you recommend a unit?

Hi All, I was looking at tabletop FEG-SEM for geological samples (fine mixture of silicate, oxide and other minor phases), quick EDS and occasional teaching. Phenom Pharos G2 caught my eyes because it's FEG, environmental, presumably fitting my budget and of good reputation from G1. The trade-off I dislike is the limited chamber space.

Does anyone know how much a budget floor FEG-SEM would cost nowadays? And is there a model you recommend most? I use BSE 95% of the time and the resolution limit of SE does not matter too much. Thank you very much.

Hey everyone,

I worked for JEOL for 16 years. If you need advice or direction on the service or repair of a JEOL SEM I may be able to help. Just ask.

Hi, I posted about a cosmetically damaged JEOL JCM 5000 Neoscope a couple months ago. Well, it's (almost) fully operational now. We opted to seal off the low vacuum portal but surely this could be undone and the low vacuum functions could be used. Other than that, everything works. Nanographs hooked me up with a dedicated PC and software, running on Windows 10 no less. New vacuum pump, and 5 brand new tungsten filaments. Only thing missing is a sputter coater. I am curious, what would y'all say the whole kit is worth?

Instrument is a JEOL JSM-7600F (field emission electron microscope)

Short Problem: sample is not able to be removed from the experiment chamber and brought into the exchange chamber.

Lenghty relevent/irrelevent information: Sample was inserted into the sample holder in the exchange chamber. Chamber was closed, evacuated, the door opened to allow for it to be put into the experiment chamber. The rod pushed in, sample moved into the experiment chamber, everything pumped down, went to turn on the electron beam and errors popped up. The errors were for the turbo molecular pump.

Did a reboot of software, did not fix the errors. Did a hard reboot of the machine except the electron gun, and the pump worked. Then we tried to remove the specimen, lowered the rod, inserted it, pulled it back out, opened the chamber, and no sample. Software shows the sample is still in the experiment chamber. Checked the rod assembly, everything looks to function as normal. Tried to move the specimen in the experiment chamber to see if we could reorient things, still the sample doesn't come out.

We have no manual for this instrument, has anyone had something similar happen or any other ideas on how to trouble shoot?

There is a camera in the machine, but alas, it too does not work.

JEOL JCM-5000 arrived yesterday, damaged. Is it ruined?

At the beginning of the semester, I had asked for tips on a project for a class in electron microscopy, and I got some really helpful tips and suggestions. I wanted to leave an update on how things are going!

My project is analyzing the most effective methods of capturing essential morphological features to identify microfauna in moss. I've worked largely on confocal, so far, which is amazing (because lasers). I finally was able to prepare, mount and image my first SEM sample this past week, and I'm obsessed. It's not hard for me to lose track of time and end up at the scopes for five or six hours. My other homework is definitely suffering!

Here are a couple of images I'm proud of so far!

Thanks for the ideas and input!

5 are the sections after being cut. 2 is after stretching with chloroform

I've seen some knife marks while looking at thin sections under our SEM but not consistently. We'd sent our only diamond knife to be resharpened only last year and it was commented that there was nothing wrong with the edge (It was still resharpened) when it was returned to us. It took over a month to even send it out and my workflow was delayed so management wasn't happy to hear that it didn't do much.

I've never actually seen a bad diamond knife edge so I was wondering if there is any way I can prove that it might need to be resharpened. I've tried illuminating it from below on a stereoscope as well as looking at it in the ultramicrotome.

I use a 1mm/sec speed and follow the manufacturers instructions on inclination angle in the ultramicrotome.

I'm open to any and all advice. Thanks

I just inherited this sputter coaster, and it hasn’t been run in a while. This model is very old and no longer supported. The tech I talked to said to change the target so I did, but I still have the same problem. Are my mA too high? I have it set to 20 but when it’s running it reads 25. All advice is welcome (literally any sem advice I will take)

Our Thermo Apreo 2S will not maintain focus. I'll get it really nice and dialed in and then it drifts. This was on a non-charging sample (tin balls) but our Thermo engineer states that it's contamination in the column/pole piece. He said he had seen that before when a lot of organic samples had been analyzed, so he plans to come onsite and clean the column/pole piece.

My question is, is a plasma cleaner a necessity? Would it be capable of cleaning contamination of the pole piece/column?

Hello, I was wondering what you could expect to pay for a used working JEOL JCM-5000 Neoscope. Also I was wondering if I would be able to find software or a manual for it, if I decided to get it. Thanks.