insightsoftwareconsortium / getyourbraintogether Goto Github PK

https://insightsoftwareconsortium.github.io/GetYourBrainStraight/HCK01_2022_Virtual/Tutorials/

As illustrated in the following screenshot, I suggest to rename the heading associated with the calendar to be agnostic to the particular iteration of the event.

https://insightsoftwareconsortium.github.io/GetYourBrainTogether/HCK02_2023_Allen_Institute_Hybrid/#agenda

-1st Get Your Brain Together Hackathon
+2nd Get Your Brain Together Hackathon

https://insightsoftwareconsortium.github.io/GetYourBrainStraight/HCK01_2022_Virtual/Tutorials/

Instructions here: https://github.com/InsightSoftwareConsortium/GetYourBrainStraight/blob/main/HCK01_2022_Virtual/Tutorials/README.md

• Update requirements.txt to use ITK 5.3 RC4, once it is tagged and wheels are available.
• link to slicer.org/wiki/Coordinate_systems and take 1 or 2 images from it and add to orient notebook
• exercise based on reorient all images into consistent orientation cell (add anatomical orientation label, let them choose the axis code)
• do super-sampling exercise (only a few missing lines)
• link to c++ example (just print spatial metadata)
• local installation instructions

@thewtex

Given the feedback we received during the Morphology working group meeting and subsequently.
Let's consider broadening ways of participation. This is what I was thinking

Ways to participate:

• Give a tutorial of your registration tools (pre-recorded or live presentation) along with example code and recipes to teach a data analyst how to run your tool and use the output on the challenge dataset and/or another open dataset
• Contribute a registration pipeline resource that can be deploy on BIL resources to register the challenge dataset (preferred) and/or another open dataset
• Come and learn about registration from experts in the field.

For the NWB hackathon, a pre-meeting meet-up was helpful for the participant to solidify their plans, meet each other and for the organizer some insight of what the participants are wanting to do and how we need to prepare for. As such we need to

• Set a please pre-register by date and have pre-meeting zoom meeting (mid -March?)
• At the meeting we present a rough calendar of daily activities etc. and each participant get a couple of meetings to discuss their plan and Q&A.

Thoughts?

@thewtex

Are you willing to entertain switching out the images in the logo with these two cells




?

Create a "do at your own pace" tutorial (a collection of jupyter notebooks)

• Introduction of the Allen CCFv3 using ITK and related tools to open and visualize the image volume - includes some background principles of biomedical imaging data
• Introduction to ITK registration framework and show examples of transform and resampling, rigid, affine, deformable
• Demonstrate the use of ANTs (on STPT - simply problem) to register one example dataset and how to use the transform output to resample the image and to transform annotation to/fro between the spaces
• Introduction of the fMOST dataset using ITK and related tools to open/visualize. Point out the specific properties/challenges of this dataset

Infrastructure to run these notebooks such as Binder, or BIL hosting