(1) Limitations


  • Map Manager is designed to import single color channel 3D .tif files. To import 2-3 color channel .tif files, the files need to be split into 2-3 separate .tif files. See our Fiji plugins to do this for you.

  • Does not handle .tif stacks with multiple repeats per images plane. Map Manager will import these stacks fine but does not know about the repeats. You want to strip out repeats before importing into Map Manager.

File name rules

  • Map Manager will have problems if any of the following strings are in your source file names:
  • _ch1
  • _ch2
  • _zs


  • Will only display one channel at a time. For most purposes this is fine. You can quickly switch between the color channels and run intensity analysis on both channels independently. To visualize a merged or composite image, use FIJI.

(2) Moving Map Manager files to another location

Moving a single-time point analysis

Move the original .tif stack along with its associated _db2.txt, _int1.txt, _int2.txt, and _l.txt files contained in the enclosed ‘stackdb’ folder.

Moving a map analysis

Move the main map file .ibw and its folder to a new location or computer.