cellorganizer-documentation_old/TODO at dev · murphygroup/cellorganizer-documentation_old · GitHub

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To Do list, in order of the documentation:

- Getting started: update with any changes since version 2.1 (4/29/14) in:
     - models supported (e.g. nuclear texture, if that's not just chromatin texture)
     - cell types supported
     - status of mentioned "planned projects"; if still planned, leave it, else could just remove that sentence
     - grants mentioned

- Overview (New section, after “About this document”): put in cellorganizer-overview-diagram with explanatory text. Citation for the image: Johnson, Gregory. 'Model Selection In Parameterizing Cell Images And Populations'. MMBios 2015. Presentation.

- Quickstart: should be removed, just a cut-off copy of "Loading CellOrganizer" right now [done]

- Installation: right now, is a duplicate of "Downloads". Should be removed if no further help is needed. [done]

- Tutorials: add links to MMBios tutorials in this section. Short blurbs about each would be helpful too. [Rachel will share Google Docs][done]

- Demos: can be broken up into more digestible chunks. Instead of having a list with all the demos, could have 3 collapsible tables: Training, Synthesis, and Other. Under each header, would have a table with columns: "Demo Name", "Demo Description". [list demos by class]
     - Basically: Demos
                  <explanation>
                  > Training
                  > Synthesis
                  > Other
     - When you open one of those tables:
                 v Training

                   | Demo Name |  Demo Description |
                   |___________|___________________|

Remove for this release
     - Image Synthesis Demos: since it's just one demo, could we just rename it "Demo 2D01 Walkthrough"? [demo]
          - also consider making the synthesized image example smaller & putting it closer to the end of the demo walkthrough

     - Training Demos: can be removed for now, since it's blank OR could add a walkthrough of a training demo (e.g. a 3D diffeomorphic demo, since it's different) [done]

- Advanced: We could add a couple of sections here, or break these off into their own:
     - Overview: a diagram with the general workflow of CellOrganizer
        - images -> parameters -> model -> sampled parameters -> synthesized images
     - Models: info about models!
        - bare minimum: their names, names of examples in cellorganizer/models, links to the papers that introduced them
        - more in depth: listing all the fields and what each means
        - could break this up into 2D Models and 3D Models subsections
    - Parameters: info about some possible training and synthesis parameters that get passed into top-level functions
        - e.g. param.seed, .numberofSynthesizedImages, .resolution

- API: add slml2img, img2slml interfaces