I’m running some tile-scan imaging experiments on a 24well labtek chamber plate with 20x objective. I’ve set up my microscope to scan a ROI in each well consisting of 6 tiles (a 2 by 3 tile scan in this well), therefore it is a multi-tile in a multi-well plate imaging experiment. For example, at well A3 tile 6, the file name I give it to each image is the following: DAPI-Well-A-3-Xpos2-Ypos3; at well B2 tile 2, the file name I give it to each image is DAPI-Well-B-2-Xpos2-Ypos1; However, it seems that Cellprofiler does not quite like that naming syntax to perform analysis of all my images.
I noticed that Cellprofiler can perform analysis on a 96well plate HCS experiment, but the examples only have one image per well. My case is similar but slightly different since I have multiple tiles in each well. Therefore, I wonder if Cellprofiler support analysis on that, if yes, how I can rename my images in a way that can be correctly identified by cellprofiler to construct a pipeline.
La Jolla Bioengineering Institute
San Diego, 92121