Importing Data

This is a recipe for the simplest import in Map Tracker. It assumes your stacks are

  • .tif format
  • all in one directory
  • the same scale.
  • all one channel

[Note] Map Tracker is able to handle stacks of different scales, multiple channels, and fused stacks.

Start with a directory of single channel 3D stacks in the .tif file format. Be sure the voxel size (scale) of all stacks are the same.

-Open the stack browser with the menu bStack -> Stack Browser
-Configure the Stack Browser to: import single channel .tif files, force a scale, rename on import, and use folder name. Here is how you do that.
Load a directory. Loads a directory of .tif stack headers into the Stack Browser. The behavior of the import is specified by the following options:

Type popup. Select ‘Generic Tiff (1 Channel).
Scope. Not used during this import
Force Scale. Make sure it is checked and fill in the x/y scale of your stacks (units are um). We are assuming all your stacks have the same z-scale (1 um).
Shorten Stack Names. Make sure it is checked and fill in a prefix for each stack. As stacks are imported, they will get new names that Map Tracker uses to file them away. In this case a81_s0, a81_s1, a81_s2, …
Use Folder Name. Make sure it is checked. This will use the name of your enclosing folder to file all loaded stacks into a Stack Browser folder/directory. This will appear as a popup in the Stack Browser (raw_lsm_aligned in the above image).

-Now press the ‘Load a Directory’ button to do the import. If all goes well, you should have your stacks in a folder.
-Select the folder with the top left popup (it will have the same name as the enclosing folder on your hard-disk). You should see a list of stacks in the Stack Browser.
-To display a stack, select it in the list and press the ‘Display Stack’ button.
-Now you have a list of single channel stacks you can import into a map using the Map Maker panel.

Note: The Stack Browser window will not display the max projection until you ‘Display Stack’. The max projection is made when you actually load the .tif file. Remember, the ‘Load a directory’ button will load the HEADERS for a directory of .tif files, it is not loading the files themselves, the ‘Display Stack’ button will load the actual .tif.

Note: To save memory, you can unload a stack by selecting it in the list and pressing ‘Unload’. If the stack is displayed, it will not unload. Loaded stacks are shown in the Stack Browser with an ‘X’ next to their name.

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