DICOM Management show-and-tell meeting

[matthew-brett]

By @ baratzz on July 12, 2021, 5:12pm

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

[matthew-brett]

By @ matthew.brett on July 12, 2021, 5:27pm

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 ...

[matthew-brett]

By @ baratzz on July 13, 2021, 3:58pm

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]

By @ matthew.brett on July 19, 2021, 11:59am

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).

[matthew-brett]

By @ baratzz on July 19, 2021, 1:58pm

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.

By @ baratzz on July 19, 2021, 3:09pm

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.

[matthew-brett]

By @ pieper on July 19, 2021, 3:23pm

@ 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.

[matthew-brett]

By @ matthew.brett on July 19, 2021, 3:34pm

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

[matthew-brett]

By @ thewtex on July 12, 2021, 8:11pm

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 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)

[matthew-brett]

By @ baratzz on July 13, 2021, 3:48pm

Hi @ thewtex,

Thanks for the reference! Please do join and share.

[matthew-brett]

By @ matthew.brett on July 13, 2021, 11:28am

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

[matthew-brett]

By @ spinorpy on July 14, 2021, 12:08pm

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.

[matthew-brett]

By @ baratzz on July 14, 2021, 12:28pm

I would like to join - if OK.

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

[matthew-brett]

By @ chafey on July 14, 2021, 6:38pm

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:

• https://github.com/cornerstonejs/dicomParser
• https://github.com/chafey/dicom-parser-rs

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

cornerstonejs.org

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

[matthew-brett]

By @ matthew.brett on July 14, 2021, 10:17pm

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

[matthew-brett]

By @ chafey on July 15, 2021, 3:04pm

Yes, I would be happy to!

[matthew-brett]

By @ pieper on July 15, 2021, 3:55pm

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.

• MGHComputationalPathology/dicomweb-client
• dcmjs-org/dcmjs
• dcmjs-org/dicomweb-client
• dcmjs-org/dicomweb-server

[matthew-brett]

By @ baratzz on July 19, 2021, 3:47pm

Fixed agenda:

• NiBabel's
  nicom
  module (@ moloney, @ effigies, @ matthew.brett)
• dcmstack (@ moloney)
• itk (@ thewtex)
• dicom_parser (@ baratzz)
• cornerstone.js (@ chafey)
• dcmjs-org (@ pieper)
• highdicom
  (Chris Bridge)

Looks like we'll have to all keep it short to cover everything.

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.