Diary

18 Mar 2020

• Meeting with Konrad's group and an introduction to Mouselight
  • Uses undertow - lightweight Jboss java container
  • RabbitMQ for messaging
  • Java as programming language
  • Jogl for graphics library
• Using Neuroglancer to align. Good place as already in use.
• Mouselight doesn't have a counterstain. Using flourescent channel to align to Allen atlas all at once.
• We need a global and local way to do a local alignment.
• Neuroglancer would send data back to python backend, lacency might be an issue. Local alignments will be more difficult. Do the global first, then do local on only a small part in space. Find a coordinate system that relates to the the images.
• Get a definitive list of steps.

11 Mar 2020

• Agenda
• Recap
• Setting priorties
• Getting existing brains done
• Getting existing pipeline working outside of docker for development purposes
• Creation of new github project to share between Litao, Sidd and Edward
• Separation of tasks for each programmer to get pipeline working with minimal code under python3

6 Mar 2020

• Split up annotating and viewing -> viewing on web, annotating locally
• Use atlas as reference to align new brains
• atlas is a blueprint of the brain, a 3D object
• take middle section of one brain and compare to atlas middle
• Annotations: Karal already has code for doing annotations.
• Test software on muralis, open set of images and draw contours on shapes
• Annotations works on stacks
• Get software and test. Neurolucida, talk to Harvey about Brainmaker
• Masking - Might use boundaries

4 Mar, 2020

• Recap
  • Update on filesystem organization
  • Update on pipeline organization
• What was accomplished the past week
  • Web server up and running with neuroglancer https://activebrainatlas.ucsd.edu
  • Birdstore file server in the process of being organized
  • Admin interface to database available at: https://activebrainatlas.ucsd.edu/activebrainatlas/admin (ask Ed for login credentials)
  • Thumbnail listing available at: https://activebrainatlas.ucsd.edu/activebrainatlas/image-listing
  • Datajoint populate method working
• Demos
  • Neuroglancer
  • Admin interface
  • Thumbnail viewer
  • Datajoint populate viewer
• What to do next week
  • Get DK43 further along
  • Get some type of project planning system for the brains. Keep track of what is going on.
  • Refine the datajoint populate methods
  • Clarify what needs to be done manually in terms of masking, ask Beth about this process
  • Get Alex's GUI implemented into the new pipeline.
  • Combine Alex terminology with help from Beth: https://github.com/ActiveBrainAtlas/Datajoint_Interface/wiki/Description-of-the-manual-processing-for-the-pipeline

26 Feb, 2020

• Litao and Ed working on database integration

• Alex moving GUI scripts into the views area

• Sid is working on Neuroglancer

  • Get forks
  • Contact the programmers, get contact info, emails.
  • Demo the sliders
  • Demo the adjusting annotations with mouse
  • New annotations

• use python libraries instead of imagemagick

• organize birdstore