Simon M. Ochs, 2013

##Abstract SpineMinerXT is a graphical user interface (GUI) for Windows embedding the image overlay processor SpineMiner. Since SpineMiner runs only on command line, the GUI was created to make SpineMining more comfortable. The basic features are implemented as Windows Forms control elements and passed as command line arguments to SpineMiner.exe. If you are not aware what SpineMiner does, you should read SpineMiner's README first: https://github.com/siochs/SpineMiner

##Building SpineMinerXT SpineMinerXT was written in C# using Microsoft's Visual Studio 2010 Ultimate IDE. It is a simple Windows Forms application. You can also build SpineMinerXT with Visual Studio 2010 Express edition which is freely available from Microsoft. To build SpineMinerXT, download and install Microsoft's Visual Studio and create SpineMiner from the build menu. After successfull build, the executable is located in the bin/ directory.

##Using SpineMinerXT SpineMinerXT requires Microsoft's .NET Framework 4 or higher. If you don't have it installed you can download it from Microsoft's web page. SpineMinerXT won't run without internet access.

###Running SpineMinerXT the first time

1. Place SpineMinerXT in the current working directory beside your .ovl files. Double click starts the Program, which extracts the embedded core application SpineMiner.exe.
2. Give the group you are going to analyze a name. As default Cohort1 is preselected. This will be the name of your database.
3. Decide if you wish to ignore spine morphologies. If so, check the according checkbox.
4. Decide if you want filopodia be treated as if they are thin spines: If so, check the according checkbox.
5. By clicking on the scientist symbol, SpineMinerXT runs the core application until the analyis is complete. A .sqlite database file will be created, by default Cohort1.sqlite. Any errors will be reported.
6. If you wish to adapt some changes, then do so according to the control elements and click the refresh picture behind the setting. This processes the database.
7. You can export your calculation results as Comma-separated values by clicking the truck. Your results will be stored as .dendrites.csv. Note: any existing file will be overwritten.

###Opening/Adapting an existing database

1. Place SpineMinerXT where your .sqlite database file is located.
2. Start SpineMinerXT.
3. Enter the name of your database (without the .sqlite filename extension, e.g. Cohort1).
4. Click the folder icon just next to it to open the database.
5. Adapt any changes you like by using the control elements. The refresh symbol updates the database.
6. Export your new calculations by clicking the truck. Note: any existing file will be overwritten.

##AutoUpdate SpineMinerXT can auto update itself. For this purpose the updater class was created. On application startup the updater is initialized with a pointer to the main form, the URL where the binary and the curr_vers.txt is hosted, the aplication name, the current version number or a file to be deleted. The system works the following way:

1. The updater contacts the host and tries to read the version number from curr_vers.txt. The host is compiled into the application. Since SpineMinerXT is downloadable as release from GitHub, a deploy release folder was created which should be updated with the newest version of SpineMinerXT and curr_vers.txt. Therefore, the URL passed to the updater is http://github.com/siochs/SpineMinerXT/releases/download/deploy/.
2. If the version inside curr_vers.txt is greater than the current version number of the application, the new executable will be downloaded from the host. The new executable is identified by the version appendix of SpineMinerXT, e.g. SpineMinerXT_1.25.exe.
3. When the download was successfull, the application starts the new SpineMinerXT with a -d option, telling the new application to delete the old one (SpineMinerXT_1.25.exe should delete SpineMinerXT_1.24.exe). When creation of the new process was successfull, the old application terminates itself so that it can be deleted.
4. The new application received the -d option and the filename of the old application. After waiting a second, the old application name is deleted. NOTE: the updater also tries to delete SpineMiner.exe from the old application.

##Updating SpineMinerXT When there will be a new release of SpineMinerXT, it will be named with the new version number appendix, e.g. SpineMinerXT_1.25.exe. 1.25 also has to be placed in the curr_vers.txt in the releases/deploy/ folder and has to be adapted in the initialization method of the form, e.g. const string app_version = "1.25";.

##Known Issues Well, if you watch the source you will agree that the whole thing is more or less hacked together to make the usage of SpineMiner comfortable for end users. Many control elements still have default names like "Button1" or "Label3"... In general I would appreciate if you have some better ideas to integrate SpineMiner in SpineMinerXT and piping it's output directly to the text box in SpineMinerXT.

##Licensing In line with the Gnu Public Licence I agree with redistribution and modification of my code as long as you do no harm.