Hi. Thanks for Cell Profiler! Can you direct me to instructions for using .flex files in CellProfiler? I have used .tif files that are independent for each wavelength, but I don’t understand how to go about building a pipeline for .flex files that seem to have all wavelengths bundled in a single file.
Ah, good question! Flex file support is still under development, but the existing functionality should be adequate. There is a note at the very bottom of LoadImages, which is the likely crux of your problem, and states “Note - If the movies contain more than just one image type (e.g., brightfield, fluorescent, field-of-view), add the GroupMovieFrames module.”
So, follow these steps:
(1) Add LoadImages module- set “What type of files…” to “tif, tiff, flex movies”
(2) Add GroupMovieFrames module
(2a) “How many frames should be extracted each cycle”. This determines the # of frames per group. For example, if your multi-frame file is grouped as ABABABAB or AAAABBBB, then the value will be 2, however if you have ABCABC or AABBCC, the it will be 3. In other words, the # of channels.
(2b) “Interleaved or separated” - Define how the frames are ordered
(2c) Settings 4 to end - "Choose names corresponding to each “wavelength”. There should be the same # defined as listed in the setting “How many frames should be extracted each cycle”
(3) Add further modules as normal
You will note that the Status Window that pops up during processing will increase as it redefines “cycles” from the number of flex files loaded to (# of files)*(# of frames extracted per flex file), which is the true number of cycles.
Let me know if this is clear, since there have not been many requests for flex file support and our documentation in this regard obviously needs some updating.