Converting raw data into Map Manager Tiff stacks

The Map Manager - Stack Browser will only import single channel Tiff (.tif) stacks and will not import proprietary image formats. Thus, all raw data must be converted using the provided Fiji plugins.

Great care has been taken to extract the voxel size, date, and time. This is critical as all annotations and analysis use um scale (not pixels) and time-series use the acquisition date and time. After using these plugins, if the voxel size, date, or time is not correct, please email Robert Cudmore and we can make them work for you.

Important: When stacks are imported into the Map Manager - Stack Browser, please verify the voxel size, date, and time are correct. If any of these are not correct, contact Robert Cudmore and we can make it work.

Rules of Map Manager import

  • Map Manager will import 3D .tif files that have been converted using the provided Fiji plugins.
  • Map Manager will not import 3D .tif files that have interleaved color channels (e.g. raw ScanImage files).
  • Map Manager will not import 3D .tif files saved as individual .tif files (e.g. raw Prairie View files).

Running the Fiji plugins

  • Either, save a plugin to your hard-drive and drag and drop it into Fiji. Once the plugin is open in the Fiji code editor, use ‘ctrl+r’ to run.
  • Or, place a copy of the plugin in the ‘’ folder, restart Fiji, and the plugin will be available from the Fiji menu ‘Plugins’.

Scope specific conversion

Zeis (lsm/czi) and Nikon (nd2) files

  • Use bFolder2MapManager.
  • Important for Nikon/nd2 import. Nikon nd2 files do not have date or time in the header. This is an egregious emmision and we are working with Nikon to fix this.

Bruker - Prairie View files


  • Coming soon.

ScanImage 3/4

  • Use bFolder2MapManager.
  • Important for ScanImage import. ScanImage 3/4 does not save the x/y voxel size in its raw .tif images as the x/y voxel size depends on how the scope is configured. You need to set the ‘magic_scan_image_scale’ variable in the Fiji plugin to correspond to the x/y voxel size when scanning at 1x magnification with images at 1024x1024 pixels. If this is not set properly, ScanImage Tiff imports into Map Manager will not have the correct x/y scale.

Fiji plugin Github repository

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

Fitting dendritic segments

This is done entirely 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.