Hello everyone, feeling stupid here.
Trying to learn cellprofiler to set up cell tracking for my timelapse videos but the software can’t ‘recognize’ my image files.
Some background here:
I acquire my timelapse images using two separate microscope systems:
(1) The first is on metamorph software which saves each timepoint as a TIF file and the metadata for the entire series as a .nd file.
(2) The second is Nikon NIS elements software which saves all data into a .nd file with no additional or separate files.
I am able to open both image files through Imaris or ImageJ to play as videos or analysis. However, as I have quite a lot of these files at various timepoints and different field of views, I want to start using Cellprofiler to automatically track objects over time.
So far, I have performed the following with no success:
(a) drag and drop images from either acquisition softwares into cellprofiler
(b) Opened .nd image file from NIS elements in Imaris and resave it as either .oem, .tif, .tif (adjustable file series) and then dragged these into cellprofiler
© dragged image files from metamorph (all tif + .nd, only tif, only .nd) and opened .nd as metadata file.
None of these work in getting cellprofiler to recognize/open these files.
Anyone have experience and can help?
Thanks very much!