Deinterleave complex series

Hi,

I’m using a microscope that runs a software that can’t save multi dimensional tifs.
It saves individual files for each position/z/channel/time so we end up with very large amount of files that is very difficult to navigate.

I can import the series with the import image sequence tool but I can’t deinterleave it.
Is there a way to deinterleave multi-dimensional series ?

Alternatively is there a better way to import multi-dimensional series ?

This is an example of series 5 channels, 2 positions, 2 Z planes

name_Bottom Slide_R_p00_z00_0_A01f00d0.TIF
name_Bottom Slide_R_p00_z00_0_A01f00d1.TIF
name_Bottom Slide_R_p00_z00_0_A01f00d2.TIF
name_Bottom Slide_R_p00_z00_0_A01f00d3.TIF
name_Bottom Slide_R_p00_z00_0_A01f00d4.TIF
name_Bottom Slide_R_p00_z00_0_A01f01d0.TIF
name_Bottom Slide_R_p00_z00_0_A01f01d1.TIF
name_Bottom Slide_R_p00_z00_0_A01f01d2.TIF
name_Bottom Slide_R_p00_z00_0_A01f01d3.TIF
name_Bottom Slide_R_p00_z00_0_A01f01d4.TIF
name_Bottom Slide_R_p00_z01_0_A01f00d0.TIF
name_Bottom Slide_R_p00_z01_0_A01f00d1.TIF
name_Bottom Slide_R_p00_z01_0_A01f00d2.TIF
name_Bottom Slide_R_p00_z01_0_A01f00d3.TIF
name_Bottom Slide_R_p00_z01_0_A01f00d4.TIF
name_Bottom Slide_R_p00_z01_0_A01f01d0.TIF
name_Bottom Slide_R_p00_z01_0_A01f01d1.TIF
name_Bottom Slide_R_p00_z01_0_A01f01d2.TIF
name_Bottom Slide_R_p00_z01_0_A01f01d3.TIF
name_Bottom Slide_R_p00_z01_0_A01f01d4.TIF

Thank you very much for your help

You could try one of the following:

  • Run Plugins › Bio-Formats › Bio-Formats Importer, point it to the first .tif file in your series, and choose the Group files with similar names option to see whether it already does what you need. See the explanations in the Bio-Formats Import Options dialog:

or, finally:

  • Keep using File › Import › Image Sequence… to read all files as a single stack, and then use Image › Hyperstacks › Stack to Hyperstack… to deinterleave with the known sizes for each dimension:

Hope that helps.

2 Likes

Hi @imagejan thank you for the tips.

I have been trying to do as you recommend but I had some issues with the 3 options.

About (1):

What seems to work best it top import them with Bio-Formats Importer with Group files with similar names option. This does create a file with the right dimensions but the issue I have is that other than the first image all the images are blanc.

About (2):

The pattern file could be a good option but if I understand correctly it would need to be rewritten every time depending on the dimensions used.

Also if I understood correctly the documentation it only works if the file name has

  • channels are called c , ch , w , or wavelength but in my case are called d
  • timepoints are called t , tl , tp , or timepoint but in my case are called p
  • series are called s , sp , or series but in my case I’m not even sure what would be the equivalent since I have grid and row & column

Finally (3):

Could be fine but this works only with series that contain only one position since it can’t a 6th dimension for the positions

Am I correct about point 2 and 3?

I feel like the Bio-Formats Importer with Group files with similar names would be the best option if it wasn’t for the blank images which I assume are a bug. How could this be fixed ?

Thank you very much