Is it possible to open Leica .lif files in CellProfiler?

I recently got familiar with CP.
Unfortunately, i have encountered one major problem. It was indicated that CP uses Bio-formats, LOCI-tools to deal with different file formats. However, i was not able to open any .lif files generated by SP5 Leica confocal microscope. Is there any way to use this file format or it is not currently supported?

Thank you very much in advance.


Even though Bio-Formats supports many formats, CellProfiler only let you see some of them. Our upcoming release relaxes these constraints on formats supported, so the .lif should be readable.

But it would be good to confirm on our end. Would you be able to post an example .lif file to make sure it can be read? If the forum balks at uploading it, you can post it as a zip file.


Thank you very much for the rapid response.
Please find the .lif file as an attached .zip archive.
The .lif file contains 3 channels and it could be open without any problem in ImageJ and BioImageXD.
If it is necessary some other information to be provided, just ask.

Thank you in advance. (6.2 MB)

Hi there,
i am still quite interested to find a solution of my problem.
Hope that you will give me some response soon.

Thank you in advance.


Our upcoming release of CellProfiler 2.1 will be able to handle these files, but the new beta won’t be available until next week. When we put out the beta, we’ll announce it.

In the meantime, what OS are you running? Mac or Windows? 32-bit or 64-bit (if Windows) or what OSX (if Mac)? Just so I can confirm that 2.1 will run on your machine…



I stumbled upon this post pretty much at the right time, as I am trying to do something similar to emiliojr.

I acquired some images on the Leica SPE3 and would like to open those in Cell profiler. I am using OS 10.7.5 (Mac). I downloaded cell profiler (2.0) about 1 month ago. Will I have to wait until the upate is released? Could I alternatively convert my lif files into something Cell Profiler can read?

Thanks, Jack

Hi Jack,

I am assuming that the .lif format is being used for containing image stacks? If so, the most straightforward alternative is to convert the .lif image stack into individual files (preferably TIF or PNG), one for each slice/channel combination.

Organizationally, you can place the individual into folders for each stack, set the Default Output Folder to the parent folder containing the rest, and set LoadImages with the following settings:

  • Analyze all subfolders within the selected folder: “All” or “Some”.
  • For each channel you specify, for “Extract metadata from where?” select “Path” and enter the following regular expression: .*\\/](?P<Subfolder>.*)$
  • Check the “Group image sby metadata?” setting and select “Subfolder” from the list that appears.

This will enable each folder (i.e, each image stack) to be processed independently from the others in CP.


Reviving this thread from 2013, I’m using CellProfiler 3.0, which lets me drag-drop my .lif file into the input region.
Problem is, when I double-click the file, CellProfiler shows me that my .lif file contains only one image, even though it contains several when I open it using Leica software.
Is this file type now supported and I’m just doing it wrong?


Hi Ron,

Try using the Metadata module’s “Import from file header” option- see that module’s help for more details.

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The Metadata module extracts some but not all of the info - especially it does not seem to extract the filenames of the individual images in the LIF file. The same info is extracted using bioformats in FIJI.
Any suggestions to what may be going on? Happy to do some troubleshooting to resolve this.