• Map Manager is designed to import single color channel 3D .tif files. For other file types (e.g. .lsm) or for other cases like 2 color channel .tif files we have some FIJI plugins that should get you started.

  • To import 2 color channel .tif files, the files need to be split into 2 separate .tif files (with _ch1 and _ch2 in their names). See bAlignBatch, a FIJI plugin that does 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.