DICOM Management "show-and-tell"

Hi everyone,

We will meet again Thursday (the 15th) at 10:00 AM Pacific time.
The meeting will be held by Zoom, use this link to join.

Excited to learn more about each other’s projects!

Best,
Zvi

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Thanks for organizing!

Shall we set up an agenda? Who’s presenting what? I’m happy to talk about the Nibabel Nicom stuff, but both Chris and Brendan are probably more up to date on those than I am …

Hi Zvi, Matthew,

If there is interest on support that could help address some of the challenges mentioned, i.e. slow parsing of large series, memory usage, etc., I could show-and-tell :giraffe: :eagle: update available in itk. These may be helpful as a resource or a backend.

For example,

import numpy as np
import itk

# Spatially sorted volume from series, for many scanners, modalities, encodings
image = itk.imread('dicom/series/dir/')

array = np.asarray(image)

image = itk.imread('multiframe.dcm')
# Individual tags
tags = dict(image)

I’ve just posted to the dicom2nifti issues in hope that the developers would be interested to join the discussion…

Hi @thewtex,

Thanks for the reference! Please do join and share.

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Gladly. If the schedule isn’t too tight, I would be happy to give a 5-10 minute demo of the general data management application (TheLabbingProject) dicom_parser was refactored from. I am working on it to support my research, which is (so far) based almost exclusively on DICOM format MRI data and questionnaire information.

@matthew.brett @thewtex @effigies @moloney

It seems like more people will be able to make it if we postpone to Monday (July 19th) at 10:00 AM Pacific time. Hope that’s alright with everyone.

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Monday 19th, 10am Pacific is fine with me.

I would like to join - if OK. I am Daniel Nanz, and I have been dabbling with Dicom, Python, Pydicom and Medical Imaging for some 20 years plus, still have an interest, but have not found the time for programming in recent years.

Absolutely, anyone who’s interested in seeing existing tools and/or presenting is welcome.

Steve Pieper pointed me to this list - while I am not a python developer, I have worked with DICOM for 20+ years and happy to help. I have developed two open source dicom parsers - one for javascript and one for Rust:

as well as cornerstoneJS - a JS SDK for displaying dicom images:

As well as WASM builds for several image compression formats (JPEG2000, JPEG-LS, etc)

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Great! Welcome, and thanks for offering. Would you like to do talk some about these in the show and tell?

Yes, I would be happy to!

While we are on the topic of open source dicom infrastructure let me point out a few more projects that may be of interest. The dicomweb client in python is very handy. Also we have packages in javascript for dicom IO and manipulation (dcmjs), and also both a dicomweb-client and a dicomweb-server implementation.

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Zvi - sorry to ask you - but do we have something like an agenda for the meeting (who goes when)?

Who is presenting the Nibabel section? Brendan or Chris - do you want to do it? Or do you want me to do it (I can refresh my knowledge).

Hi,

I wrote down a random order to ask everyone to present in (I’ll send it in a bit when I get home). If there are any preferences please let me know.

So, I was thinking something along:

  1. NiBabel’s nicom module (@moloney/@effigies/@matthew.brett)
  2. itk (@thewtex)
  3. dicom_parser (@baratzz)
  4. cornerstone.js (@chafey)
  5. dcmjs-org (@pieper)

Does this make sense? Hope I didn’t forget anyone.

@baratzz - That looks good, and also Chris Bridge said he would be a able to present about highdicom. Looks like we’ll have to all keep it short to cover everything.

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I was also hoping to hear from Brendan about dcmstack. Brendan - OK with you?

Fixed agenda:


Absolutely. It is certainly going to be a challenge.
I think if we really don’t manage to keep things within a reasonable timeframe, the JS and higher-order packages (i.e. highdicom) might have to be postponed to a second meeting, but I’m still hopeful. We’ll see how we do.

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