Stack Browser

The stack browser is the main starting point for using Map Manager. The stack browser provides an interface to load and browse folders of .tif stacks.

Open the stack browser from the main menu ‘MapManager → Stack Browser’.

The list on the left is a list of loaded folders. Select a folder (on the left) and the list on the right will show the individual stacks within that folder.

To display a stack:

  • Right click the stack and select ‘Display Stack’
  • Select the stack and hit d for ‘D’isplay.
  • Double click a stack

Loading stacks

Load Tiff Folder

Load a folder of single channel .tif files from hard-drive. If these .tif files have been converted with one of the Map Manager Fiji plugins, the voxel size, date, and time should be correctly set.

ScanImage Import - Load ScanImage Folder

The Load ScanImage Folder loads a folder of ScanImage .tif stacks.

Important. When importing ScanImage .tif files, the scale is not set by ScanImage. You need to calculate your x/y voxel size (in um per voxel) when you scan at 1x magnification with 1024 by 1024 pixels. You then set this value in '2p um/pixel (1024@1x)'. Map Manager will use this value to calculate each stacks x/y scale for arbitrary ScanImage zoom settings.

Canvas - Load Canvas

The Load Canvas load an entire canvas of an imaging session. The canvas includes both video snap-shots and the location of two-photon imaging stacks. Please see the canvas documentation for more information.

Drag and drop

A simple way to load a single stack is to drag and drop a .tif file onto the Igor program icon. Stacks opened with drag-and-drop will appear in a special folder named ‘DragAndDrop’.

Displaying stacks

Select a folder on the left and the stacks in that folder will be shown on the right.

Display a stack:

  • Double click a stack
  • Right click the stack and select ‘Display Stack’
  • Select the stack and use keyboard d for ‘D’isplay.

Unload a stack:

Once a stack is displayed, it will remain loaded until it is explicity unloaded with keyboard u. In this way displaying a stack is faster as the stack does not have to be re-loaded.

Sorting stacks

The order of stacks can be sorted by selecting columns in the stack list. To sort by date, select ‘Date’ in the columns header. This ordering is critical when batch importing a list of stacks into a Map Manager map.

Right-click a folder for a context menu

  • Unload Folder. Unload the folder and all its stacks.

  • Stack Report (all stacks). Generate a stack report for all stacks.

  • Segment Report (all stacks). Generate a segment report for all stacks.

  • View Database (all stacks). Generate a table with all analysis. This can be copied and pasted into other programs for analysis.

  • Intensity Analysis (all stacks). Analyze the intensity of all stacks in the folder. It is critical that each spine in the analysis is checked manually. Please see [Intensity Analysis][intensity].

  • Save all stacks. Will save the annotations for all ‘dirty’ stacks in a folder. Dirty stacks are stacks that have been changed or modified since they were loaded. Dirty stacks are noted in the stack list with a red background in the ‘D’ column.

  • Unload all stacks. Unload the raw image data for all stacks in the list.

  • Show Folder On Disk. Open the hard-drive folder the folder was originally loaded from. This opens a Finder window on OSX and an Explorer window on Microsoft Windows.

  • Refresh List. To refresh the list of folders and the selected folder’s list of stacks. This is generally not needed.

Right-click a stack for a context menu

Right-click a stack to open a contextual menu. These menu items can also be triggered using the indicated keyboard shortcuts.

  • Display Stack. Open a [stack][stack] window. Same as double-click.

  • Unload Stack. Unload the raw data for a stack. Important, this unloads the raw data to conserve memory, it DOES NOT unload the stack annotations.

  • Unload Stack DB.

  • Stack Info.

  • Stack Report.

  • Segment Report. Generate a segment report for all segments in a stack. See reports.

  • View Database. Open a text table with all annotations in the stack. This can be copied and pasted into other programs for analysis.

  • Experimental - Segment Length Plot. Make both 2D and 3D plots of segment length as a function of the Z-Smoothing parameter.

Right-click headers in the stack list for a context menu

This menu will toggle the columns that are displayed in the stack list. These setting are saved with the main Map MAnager Options.

What is next?

Once a folder of .tif stacks is loaded