BaSiC plugin for illumination correction on Airyscan timelapse movies

Hiya,
I want to correct my Airyscan movies for illumination variation/jumps and I am trying to use teh BaSiC plugin from ICB,
I have a single tif file with all the timepoints. (separated the H2B channel)
However, it seems it is not recognized by the plugin which requires an image stack.
Does this mean I will have to convert aaaaalll my movies into single images stacks (which TBH I would not do)? or is there a quick fix / tip to use a single tif with all the timepoints?
Anyone from ICB on here?
cheers
Debbi

Hi Debbi,

I am Lorenz, a student working with Dr. Tingying Peng and Dr. Carsten Marr from ICB, the developers of BaSiC.

Do I get you correctly that you have one large .tif file containing a movie with a single color channel? I feel like, this should not be a problem for BaSiC to process. Could you provide sample data, so we can see ourselves what the problem is and try to get it running?

Best,
Lorenz

Hi Lorenz,
thanks for the reply - my tif file has 2 channels but I want to adjust on one channel only (so I can have a laaarge tif file with single channel and multiple timepoints - around 170-200).
The illumination has jumps and I wanted to see if BaSiC can correct this.
I will send you a message with a download link.
Cheers

Debora

Hi Debora,

thanks for sending the file. I had a look and it seems like BaSiC has a problem when dealing with time points; it only recognizes the first time frame and thus thinks that there is only a single image open.

As a quick workaround, you can try to use Fiji’s ‘Properties…’ function to let Fiji view the movie as a stack, i.e.:

  • Open the movie in Fiji
  • Image --> Properties…
  • Switch the numbers of ‘frames’ and ‘slices’

When using your sample data, this worked for me. However, this is not very elegant. We are currently working on adding new features to BaSiC and hopefully can fix this issue in the next version.

Let me know if this solution works for you and whether BaSiC can help with you illumination problem.

Best,
Lorenz

Hi Lorenz,

this trick seems to have done it! thanks!!
Debbi