New menu item in front page navigation bar

[rjdodson]

Please add a new menu item in the front page navigation bar "Cell tracking". Place the new menu item between "Tools" and "Explore".

Background:
Dave Knecht has provided two utilities which he requests that we display on dictyBase.

1. Track Maxima- A FIji/ImageJ plugin that automatically tracks cell positions in time lapse image sequences. Very configurable and does a better job of tracking cells than anything else I have tried besides manual tracking (mTrackJ in ImageJ). I have primarily used it for phase contrast images, but it should work for other image types as well.

2. Excel Macro template for quantifying and plotting the data measured by Track Maxima or mTrackJ plugins.
   You copy and paste the position data (Display Full Track Table from Track Maxima or points from "measure" in mTrackJ) and paste the data into the Excel spreadsheet. The macro separates the data for each cell, tracks their speed and directionality and plots the data. I will put together a more full featured instruction set with examples when I have time. You can give my address for questions as I am likely the most experienced user available to help people. I will work on the instruction sheet this week. Dave

Sidd's instructions to display this data:

1. Open a GitHub issue in the dictyBase/frontendx repo. (https://github.com/dictyBase/frontendx)

2. Request a new menu item in our navigation bar. Choose where it fits best.

3. Make a new page explaining the tool, its content, and how to use it.

4. Ask for a link to that page in the new menu item.

5. Get the Excel macro template from Dave and put it on our server. We don't have a file-upload tool yet, so request one. Upload it, and the server will create a link for the page.

6. Let Kevin know you need this.

7. Done.

[rjdodson]

As Rex commented at the meeting, we should not add this as a separate menu item. Instead add it as part of the tools menu. Add it right after "genome browser".

[ktun95]

Hi Bob,

Are the links to these utilities available yet?

[rjdodson]

Hi Kevin: no not yet. I'm working on a page explaining the tool but haven't made much progress yet. David Knecht will also provide some instructions but he hasn't sent these yet either.

But I think the real challenge will be linking to the utilities-that is a functioning version of TrackMaxima and the excel template. Dave sent the TrackMaxima as a TrackMaxima_jar.zip file which I can download but not open due to it being an unsupported format. So I think I will eventually need your or Sidd's help opening that file and getting all of this to work. I'm not sure how to assign this as a priority within our workflow needs, but I know that getting the website out is most urgent.

If you have any additional thoughts please let me know.

[rjdodson]

In this comment I am requesting a file-upload tool as mentioned in step 5 in Sidd's instructions below

5. Get the Excel macro template from Dave and put it on our server. We don't have a file-upload tool yet, so request one. Upload it, and the server will create a link for the page.

In his original email to me, Dave sent the Excel macro template Sidd is referring to, and I have it in my downloads folder as file name:

Chemotaxis template v16

I think creating a file upload tool can be done as an independent side task while Dave and I are working on a page explaining the tool. And we will also need to look into opening the TrackMaxima_jar.zip file in order to generate the position data for the template file.