Things to do for tracking software paper

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Things to do for tracking software paper by Mind Map: Things to do for tracking software paper

1. Create

1.1. Write code

1.1.1. Almost done, Steve thinks, at least for version 2010

1.1.1.1. Tweaks definitely will be needed, but not a big deal, I don't think

1.1.1.1.1. Biggest tweak is how to append and save data

1.1.2. Automation seems to be working fine. Load 2-d raw data added to mother program as well as the ability to look at the paths of any .dat file in a folder

1.1.3. Possible Tweaks to Convolution Program

1.2. Test code

1.2.1. Test on real data (doing this with Andy already)

1.2.2. Test on simulated data--using Larry's slick MT image generator -- this is exciting and probably very powerful for the paper

1.3. Graphs

1.3.1. Comparing tracking data to known information from convolution program

1.3.1.1. Faux microtubules going in different paths (horizontal, vertical, sloped line, circle, some combo) at different speeds and different brightness and different sizes and background noise

1.3.2. Show actual data from Andy's videos

1.4. Pictures

1.4.1. Microtubules and tracks from automation

1.5. Compare code?

1.5.1. I learned from the Hand et al. reference that ImageJ has a tracking plug-in called (MTrack2)

2. Contribute

2.1. Paper

2.1.1. Write paper

2.1.2. Submit paper

2.1.2.1. Most likely PLoS ONE for refereed pub

2.1.2.2. Nature Precedings

2.1.2.3. UNM Institutional Repository

2.2. Place code in public; usable

2.2.1. Code must be relatively clean but doesn't have to be too clean

2.2.1.1. As an example, The cleaning that Larry did for the tracking subVI helped a bunch and is sufficient

2.2.2. Compiled version will require a license to run

2.2.2.1. Can talk with Malloy to see if his brother (brother in law) can get us some special NI deal so people can run our code for free? Perhaps a license that expires?

2.2.2.1.1. 2/2/2010 Steve sent email to Malloy

2.2.2.2. Virtual machine possiblity (Deepak advice at #scio10)

2.2.2.3. Also possibility of remotely logging in to our own server

2.2.3. Data posted on IR?

2.2.3.1. Test data (real and simulated)

2.2.3.1.1. Meeting with Amy next week and will discuss this possibility

2.2.4. Create screen cast to demonstrate how to use

2.2.4.1. Storyboarding would help

2.2.5. Code to Possibly Make Pulbic

2.2.5.1. Mother Tracking Program

2.2.5.2. Automation Tracking

2.2.5.3. Convolution Program (?)

2.2.5.3.1. This is no where near cleaned up

2.3. Poster

2.3.1. only take up part of the poster

2.3.2. Pictures

2.3.2.1. automated path picture is pretty sweet

2.3.2.2. diagram of code

2.3.2.3. data

2.3.2.4. frames with ROI around microtubule that is being tracked

2.3.3. If this was taking up more of the poster i would think about testing it with the convolution program but that might take some time to get running and I might not have it before San Fran