nilseling
commented
2 years ago Hi @sittnerr
the CellProfiler pipelines in this repository do not read in .ome.tiff files. Simple .tiff files are sufficient. If you only acquire 3 channels (I assume you have one nuclear and maybe 2 cytoplasmic markers) you could skip the ilastik classification step and apply a simple segmentation approach directly using the intensities. As for image alignment, this is not supported by the pipeline. Please reopen this issue if there are more specific questions regarding the ImcSegmentationPipeline. Best,
Nils
Hey! I am using the Zeiss Observer Fluorescence microscope to take pictures in three different channels a day for four consecutive days to map out the tissue similar to IMC (multiplex method)! I can export my files as ome.tiffs and was wondering if it is still possible to insert these ome.tiffs into the pipeline starting after the conversion of the mcd to ome.tiff images - the metadata in the ome.xml file looks slightly different using other descriptions but shouldn't it still be possible with alterations in the code to extract the necessary data? this is an example how the channels are listed in the xml file for one tiff file containing three channels - goal is to stack each three channel image from the different days, align them and segment them in order to use histocat for analysis