Fiji plugins

Converting stacks to open in Map Manager

Map Manager has a number of custom Fiji plugins to convert raw image stacks into a format that can be imported into Map Manager.

Map Manager will open 3D .tif image stack with 1, 2, or 3 color channels.

  • Map Manager will not open 3D .tif files that have interleaved color channels.
  • Map Manager will not open 3D .tif files saved as individual .tif files (Like with Prairie View).

Please see the Fiji Plugins Github repository for the most recent version of each of these plugins.


Use bFolder2MapManager

ScanImage (ScanImage/Vidrio)

Use bFolder2MapManager

Prairie View (Bruker)

Use bPrairie2tif

In all these plugins, great care was taken to extract the voxel size, date, and time. This is critical for rapid workflows to always score annotations in um and to make time-series in the correct order. If the voxel size, date, or time is not correct, please contact Robert Cudmore directly and we can make them work for your raw data.

Important: When stacks are first imported into the stack browser, please verify the voxel size, date, and time are set correctly.

Fitting dendritic segments

This is done seemlesly from within Map Manager and only requires an installed Fiji program to be specified in hard drive paths.

The Map Manager code to fit dendritic segments is a modified version of the Simple Neurite Tracer Fiji plugin.

Exporting stack annotations to Fiji

A Fiji plugin (bMergeChannels) is provided to open all annotations and segments in a stack into Fiji, displaying them in the Fiji ROI manager, 3D viewer, and in Simple Neurite Tracer.

  • From a stack window, select the main menu ‘MapManager - Experimental - Export To Fiji’. This will generate a number of text files in a folder named ‘MapManagerExport’ on the desktop.
  • Open Fiji and drag and drop the ‘’ plugin onto the Fiji window. The plugin is in the main map manager source code in the ‘Tracing’ folder.
  • In Fiji, run the plugin and select the .txt file corresponding to the stack that was just exported. The plugin will display the stack, all annotations in the ROI manager, and display a 3D view of the stack with line segments and annotations included.
  • The tracing can also be opened in Simple Neurite Tracer. In Fiji, with the stack window frontmost, select ‘Plugins - Segmentation - Simple Neurite Tracer’. In Simple Neurite Tracer, load the .swc file (in the MapManagerExport folder) corresponding to the stack that was just exported.