Announcing NimPulseq - A Nim port of PyPulseq with a protocol editor GUI that can run on your scanner

[fsantini]

Dear Community,

(First of all, sorry for the cross-posting with the pulseq repository, but I don't know how much overlap there is between the followers of both pages)

I am happy to announce NimPulseq and NimPulseqGUI, a port of (Py)Pulseq to the cross-platform, statically compiled language Nim.

Why, you ask? Well, there are various reasons:

• Nim compiles to a single executable file without library dependencies: You can distribute your sequences in a single executable format that, when executed, creates a .seq file. This allows changing sequence parameters from the command line, so creating multiple versions of the same sequence is easy. If you want, you can avoid releasing the source script that generates the .seq file (note: I do not recommend doing this, but you do you), and still provide your users with a sequence that adapts to multiple systems, without having to generate a .seq file for every system yourself.
• Create .seq files directly on the scanner: Since Nim is multi-platform and dependency-free, you can execute the compiled script directly on the scanner, and change parameters directly at the scanner console.
• Nim is faster: writing a .seq file from a compiled Nim script is up to 50 times faster than PyPulseq (based on the write_gre example)
• NimPulseq comes with a native cross-platform GUI that can be run on the scanner: using NimPulseqGUI, you can bundle the executable with a GUI that can pop up on the scanner, so you can tweak your parameters as you would with a "normal" sequence (see below). Binary search and protocol validation is automatically implemented in the GUI. The GUI has no dependencies under Windows, and depends on GTK3 under Linux/Mac. Setting up the GUI is extremely easy. Basically, you just need to tell the package which parameters you want to change, and then it takes care of everything. The output is a single exe file that contains your adaptable sequence.
• For Siemens (NX) Systems, you can run the NimPulseq protocol editor as a step in a scanning protocol using the ExeRunner dummy sequence available on the Siemens Teamplay platform.
• It is statically integrated with the PulseqSystems package, so you can run your sequence with mysequence.exe --manufacturer="Siemens Healthineers" --model="MAGNETOM Prisma" and the Opts structure is automatically adapted to the scanner

The drawback? Well, the main drawback is that it's a different language from Matlab and Python. AI should do a good job in converting your existing sequences to Nim, should the need arise. However, although Nim is statically typed, it requires far less boilerplate than C/C++ while maintaining its speed and lightness, and it's not more complicated than Python to learn.

Final notes

• NimPulseq itself is completely based on PyPulseq, and converted with a strong help from Claude Code, so most of the credit goes to the original PyPulseq devs.
• Examples and tests are ported too, and they pass.
• Reading sequences, simulation and plotting are not implemented.

Check out the repositories or drop me a line if you want to know more.

Cheers,

Francesco

[JosephGWoods]

Hi Francesco. This is a very cool idea for being able to adapt sequences at the scanner. Thanks for informing me of the ExeRunner dummy sequence too, which I didn't know about.

One question I have is couldn't you just make a GUI for your pypulseq sequence and compile the whole thing using PyInstaller? In this case, what is the advantage of a compiled Nim application vs a compile python application (apart from that you've already done all this work to make a nice Nim solution)?

[fsantini]

Hi Joseph! Yes that's in principle possible, but apart from the large overhead that pyinstaller has, I haven't had success in properly signing pyinstaller binaries to be executed on the scanner, especially when they include GUI libraries like pyqt. But of course feel free to do so :)

You hadn't heard of Exerunner because I uploaded it to teamplay a couple of weeks ago :)

[JosephGWoods]

Okay, thanks Francesco! I haven't tried it so was just interested in the practicalities. Have you tried py2exe? I don't know if that has any effect. Do you have any idea what the signing issue is with pyinstaller binaries if you can run Nim binaries?

[fsantini]

I haven't tried py2exe. If you make a single exe with PyInstaller, it gets decompressed inside a temporary folder, so that wouldn't work, because the decompressed dlls would not be signed. You then need to create a "folder" distribution instead of onefile, and then sign all the binaries (exe and dll) inside that folder and subfolders. It might eventually run, but when I tried it in the past, it didn't work. And the end result is really big and bloated.

[fzimmermann89]

out of curiosity: would something like Exerunner be possible for VB as well?

[fsantini]

Yes, absolutely! Backporting should be quite easy. The windows code should stay mostly the same, you will need to adjust the folder locations, and of course the little IDEA quirks.

[fzimmermann89]

An alternative i tried out of curiosity is fzimmermann89/pulyseqeditor#1
you can download it here:
https://github.com/fzimmermann89/pulyseqeditor/actions/runs/24158254130/artifacts/6337063699

this is a single exe pypulseq py->seq "converter"
it uses pyodide to run numpy etc without having to extract any files to disk.

[fzimmermann89]

there is also a basic "gui" version using webview. currently, it is a python code editor. but in principle, it could be any react GUI. so it could also be a custom gui for the sequence to only set some parameters like you did in zig

[nathanielatom]

This is awesome!! I had the same idea (https://pyscript.com/@atom137-1/pypulseq-pyscript/latest?files=main.py) if there's anything you want to use from my prototype. I think a local web-based (not necessarily online) version would be portable, convenient, and secure given the context of scanner systems. I can confirm the exe CLI above works on a Windows 10 virtual machine (with the typical unsigned executable dialog https://learn.microsoft.com/en-us/answers/questions/4299972/i-get-the-windows-protected-your-pc-message-is-my).

I created a decorator scalar_parameter in the above pyscript which wraps the main function in PyPulseq examples. The idea is that whoever initially programs the sequence can easily define a subset of function parameters along with ranges and steps (for example @scalar_parameter('flip_angle', [0, 180], 0.1, unit='deg')), and that can be used to construct a sequence-specific GUI for other users (on the scanner) to adjust with sliders (for now all it does is set corresponding definitions in the .seq file).