SerialEM Note: Early Adaption To UTAPI

Author:

Chen Xu

Contact:

<chen.xu@umassmed.edu>

Date_Created:

Jan. 24, 2026

Last_Updated:

March 5, 2026

Abstract

Around mid-2025, Thermo Fisher began shipping their TEM platform software with the Universal TEM Application Interface (UTAPI). This is a new scripting interface built on its own framework, independent of the earlier Standard Scripting and Advanced Scripting frameworks.

On both our Talos Arctica and Glacios systems, the UTAPI server is included with platform server version 7.22. It was said the UTAPI will be the only scripting interface eventually.

SerialEM immediately supported it. It currently supports all three scripting interfaces - Standard Scripting, Advanced Scripting and UTAPI. They can all run at the same time.

As one of the early adopters, we have been experimenting with UTAPI using the latest version of SerialEM. In this note, I describe what is required to use UTAPI.

In Property File

If your system comes with UTAPI, which you can check the existence of the folder:

C:\Tecnai\Exe\UTAPI

Also, in “Microscope Software Launcher - Messages”, there should be a line like:

2026-02-02 | Talos | Starting 'UtapiServer' service

You can start to use by adding some new property lines in your property file.

In main section (before any camera properties), you can add there a few lines

UseUtapiScripting     1      # 0 -> disable
UseImageBeamTilt      1      # need to have this with Utapi, otherwise BeamTilt is in different definition!!!!
SkipAdvancedScripting 0
SkipUtapiServices     0 2-19 21-32   # except Aperture(1) and camera (20)

In Falcon camera section, there are lines in the property:

Name            Falcon 4i
DetectorName    0 EF-Falcon
## for UTAPI
UtapiName       Falcon 4i EnergyFilter
UtapiLocalFramePath       Z:\
FEICameraType   6
## For Advanced Scripting, using \\192......
FalconLocalFramePath      Z:\        # \\192.168.10.81\OffloadData\TemScripting\EF-Falcon
FalconRemoteFramePath     Z:\        # \\192.168.10.81\OffloadData\TemScripting\EF-Falcon
FalconGainRefDir          Z:\ImagesForProcessing\EF-Falcon\200kV

What If There Is A Problem

It seems at this time, the UTAPI is not quite solid yet. We have bumped into situation the beam tilt control and stigmator were not working. You can simply turn off the specific services of UTAPI, and let Standard Scripting and Advanced Scripting do the routine work. This is a mixed use case. You do this by the line:

SkipUtapiServices         0 2-19 21-32   # except Aperture(1) and camera (20)

In this case, only Aperture control and Falcon camera are using UTAPI services, all the rest are not being used (skipped). The skipped ones are still using Standard and/or Advanced Scripting.

How do we know what number is referred to which service? David’s code has this portion to help. I listed them here:

## index for Utapi support for skipping service (mainly for testing purpose)
## https://raw.githubusercontent.com/mastcu/SerialEM/refs/heads/master/SerialEM.h
#UTSUP_DEFLECTORS1 = 0,
#UTSUP_APERTURES, 1
#UTSUP_NORMALIZE, 2
#UTSUP_BEAM_STOP, 3
#UTSUP_BLANKER, 4
#UTSUP_COL_MODE, 5
#UTSUP_FLUSCREEN, 6
#UTSUP_FOCUS, 7
#UTSUP_ILLUMINATION, 8
#UTSUP_MAGNIFICATION, 9
#UTSUP_PHASE_PLATE, 10
#UTSUP_STIGMATOR, 11
#UTSUP_FLASHING, 12
#UTSUP_STAGE, 13
#UTSUP_HIGH_TENSION, 14
#UTSUP_COL_VALVES, 15
#UTSUP_VACUUM, 16
#UTSUP_VAC_CHAMBERS, 17
#UTSUP_XLENS, 18
#UTSUP_FEG, 19
#UTSUP_CAM_SINGLE, 20
#UTSUP_ACQUIS, 21
#UTSUP_STEM_RASTER, 22
#UTSUP_STEM_DYNAMIC, 23
#UTSUP_CAM_CONTIN, 24
#UTSUP_LOADER, 25
#UTSUP_SAMPLE_TEMP, 26
#UTSUP_COLUMN_TEMP, 27
#UTSUP_VIBRATION, 28
#UTSUP_FILTER, 29
#UTSUP_TEMP_CONTROL, 30
#UTSUP_CAM_INSERT, 31
#UTSUP_DEFL_ALIGN, 32
#UTAPI_SUPPORT_END

I manually added the sequential numbers here for the index.

You can also just not use UTAPI at all, but you don’t have to do that.

UseUtapiScripting         0

For more details, please refer to the help file. Currently, some new features are only available through UTAPI, and this will become increasingly true over time. Thermo Fisher is no longer developing older scripting interfaces.

For example, the Falcon 4(i) camera can output compressed TIFF files using LZW compression for raw frames, similar to the Gatan K2/K3 cameras. This can significantly reduce file size. However, this option does not provide super-resolution capabilities like EER. It is more comparable to the “Bin counting by 2” option on the K3 camera. If you acquire images with some degree of oversampling and apply Fourier cropping during processing to reduce aliasing noise, this approach may be sufficient in some cases.