I want to input deconvolved images (32bit float tifs) into CellProfiler for my analysis pipeline but somehow it doesn’t seem to work and I can’t find the issue.
Images are originally ics files output from huygens. Then I wrote an imageJ macro to max project them and save them as a 4-ch tif (specifying the display ranges for ease of use). I can open them fine on Fiji (so I guess BioFormats works).
I input htem in the pipeline and the metadata extraction + regex works and recognizes that there are 4 channels and 1Z
But when I want to run the NamesAndTypes module and assign channel names it doesnt work --> “Your pipeline doesn’t produce any valid image sets as currently configured”
Any ideas? or should I force the 16bit conversion?
am a bit worried about how the rescaling will work in case of 32bit float images (what max will CP use?)
Fiji Min/Max information on each channel
Fiji Informtion output on the images
Title: 20201119_514_UNTR_Rep2_02_cmle_Max.tif Width: 81.92 microns (1024) Height: 81.92 microns (1024) Size: 16MB Resolution: 12.5 pixels per micron Voxel size: 0.08x0.08x0.262 micron^3 ID: -13 Bits per pixel: 32 (float) Display ranges 1: 0-35000 2: 0-90000 3: 0-80000 4: 0-105000 Frame: 4/4 Frame interval: 1 sec Channels: 4 Composite mode: "composite" No threshold Magnification: 0.75 ScaleToFit: false Uncalibrated Path: D:\_INPUT\WF_data\siLap2_siBAF_replicat1-2_decon\Untr_Replicat2_decon_Max\20201119_514_UNTR_Rep2_02_cmle_Max.tif Screen location: 579,108 (1920x1200) Coordinate origin: 0,0,0 No properties No overlay No selection