Future Feature / To Do List

[rhysgirouard]

• Add windows supported script
  • install VM and windows MATLAB
  • write scripts for calling fiji
  • verify that windows version works
• Restrict to only 4 steps (or change oligomeric state code to compute more)
• remove unused code files from github
• more dynamic zoom windows
• better hotkeys (don't put quit so close to zoom)
• subtract background
• check cropping effect
• adjust for laser intensity
• reduce noise
• add fail checks to fiji code
• provide counts for seen/unseen traces
• demonstrate effect of quality threshold
• easier setup adjustment
• gui?

[rhysgirouard]

• add example raw and fully processed to github
  • Files are just very large and not worth putting here while testing

[rhysgirouard]

• streamline code to remove repetitive lines

[rhysgirouard]

• speed up code
  • import image only once
    • Can't keep all images in a temp variable because that is too big
    • might only need to import a few frames for first frames creation
    • try fully processing images one at a time instead of processing in chunks
  • make only necessary plots

[rhysgirouard]

• make plot use UI on first graph

[rhysgirouard]

• convert to a MATLAB app

[rhysgirouard]

• improve function names (use verbs to make code more clear)

[rhysgirouard]

• streamline code to remove repetitive lines

I have removed repeated stuff from figure generation

[rhysgirouard]

• Make sure that figures don't steal focus when created (hide them or pre create and update?)
  • Now only steal focus at very end( not sure how to improve from this)

[rhysgirouard]

• Fix multiple input parsing for fiji code (will error on files ending in z)

[rhysgirouard]

allow file paths with spaces

[rhysgirouard]

• use ImageJ-MATLAB everywhere instead of Miji and IJM
• stop ImageJ from stealing focus

[rhysgirouard]

• fix all the addpath savepath javaaddpath stuff?
  • should not have to have another version of the jars in GitHub the code should find them where they are normally stored
  • should probably not savepath?

[rhysgirouard]

• test direct image access to save space and make code more direct

[rhysgirouard]

• make figures pause key press detection to prevent multiple quick key presses from causing code to bug