MuVi SPIM_Convert_Tools - MontpellierRessourcesImagerie/imagej_macros_and_scripts GitHub Wiki

The Muvi-SPIM-Convert_Tools help to convert your hdF5 files comming from a MuVi-SPIM setup. The source code in git-hub can be found here.

Aim

  • allow to convert 3D timelapse in Maximum Intensity Projection (MIP) with a X&Y Crop
  • Possibility to choose between Cam_Left, Cam_Right and Fusion data
  • save in TIFF or h5 format

Getting started

  • Download the macro Place this file inside the "macro" directory of ImageJ / FIJI.

  • Launch the .ijm macro To do so, first go in Plugins->Macros->Install and choose the .ijm, then go in Plugins-> Macro-> MuVi-SPIM_Convert_Tools.ijm

Features

Choose the camera Left and/or right or fUSED images (from the luxendo/brucker fusion software)

1.Montage

Then choose the folowing options :

  • the output format (tiff or h5)
  • the resolution (only for fused images)
  • the option MIP (Maximum intensity projection)

2.SaveAs