Displaying multi timepoint tiff files

Image Analysis
#1

Hi!

I’ve been successfully processing multi-timepoint tiff files produced by Incunosys Zoom system in CellProfiler. It recognizes tiff-files’ multiple timepoints and I get out very nice data.

However when I try to process results in CellProfiler Analyst I ran into following issue.

It seems that opening images for classification or in image viewing produces following error

An error occurred in the program:
JavaException: For input string: “1,219998”

Traceback (most recent call last):
File “cpa.py”, line 287, in launch_image_viewer
File “imageviewer.pyc”, line 227, in init
File “imageviewer.pyc”, line 675, in OnOpenImage
File “imagetools.pyc”, line 52, in FetchImage
File “imagereader.pyc”, line 29, in ReadImages
File “imagereader.pyc”, line 46, in read_images_via_cp
File “bioformats\formatreader.pyc”, line 470, in load_using_bioformats
File “cellprofiler\utilities\jutil.pyc”, line 308, in run_in_main_thread

Does this mean that tiff-format that I’m using is not supported or do I need to tweak some settings in .properties file? I already tried image_size_info = Y and N but it did not help in this.

Is a good “plan-b” to this that I somehow split the tiff files to individual frames and then name of the frames can be found from database CPA uses?

Best regards
Tero Heikkinen
University of Oulu
Finland

#2

Hi Tero,

Yes, I’m afraid that your Plan B is necessary. CellProfiler Analyst is not set up to process anything about time-lapse images or any stacked file formats. CPA will treat each image individually. So yes, if you think it will be useful, I would indeed suggest exporting as individual tiffs – in fact, I would suggest that the most streamlined approach would be to export as individual tiffs initially, and then process those in CellProfiler and finally CPA. This way the output database files and properties file can be read into CPAnalyst without any user intervention.

Cheers,
David