Summer 2018 Research Goals

Make Caster Usable

• 3D Model OR export in TrakEM2 format
• Load an entire stack
• Automatic Membrane Following
• Make an actual tool (Automated Brushes Menu?)
• Script to prepare an image stack
• Save alignment and metadata

Submit a paper for publication

• Gus's stuff
• Automatic Membrane Following
• Membrane seeking
• Janey's stuff

1. Seth will decide how many papers based on what Gus and Janey did
2. Seth will make an outline of the paper(s)
3. Previous Work study needs to happen (results from last Summer, anything new)
4. Algorithm descriptions for automatic membrane following and other automatic segmentation tools
5. User guide (maybe not part of the actual paper)
6. Results section needs to compare with other and previous tools, using many pictures
7. Reviews of paper draft (Pete, any other author we've included stuff from like Janey or Gus)

Pete's New Program for Light Microsocopy (PNPLM)

1. Plan framework and pick QT vs. GTK
2. Develop plugin framework to add tools (NOT plugin in the precompiled sort.)
3. Set up basic program and confer with Pete
4. Add tools as required
5. Prepare paper introducing the program
6. In parallel with previous: Solicit feedback from other labs