Hello, using CP 2.1.1 on OSX. Could use some help with a problem in using CP to process image stacks. We run short time lapse image capture at 100 Hertz. We would like to quantify the area under the nuclear (DAPI/Blue) mask in the Green image. Problem is, in Names & Types CP attempts to pair everything. Ideally we would like to generate a single mask and be able to reference it for 600-700 images without reprocessing the nuclear mask. Could you recommend a routine to achieve this? Maybe we could export a binary mask of the nuclear segmentation in one pipe and then write a second pipe to read it in and apply it to Green images? We have been trying something like this but are having trouble with retrieving images as the functions provided to read in images inactivates the auto file-loading, metadata, names and types, and grouping functions. Any help would be greatly appreciated.
Yes, you can do this, if I understand correctly. In NamesAndTypes load in your channels to be masked per usual. Then at the bottom of the settings of NamesAndTypes, choose the “Add a single image” button. The image you choose here can be used for, say, an illumination correction function or a single mask, as you desire. Then you can choose a module like MaskImage and load in the image mask, gotten from, say, thresholding the single input image. I added an example project file adapted from the ExampleFly image set from the first link in the Welcome Screen.
Let us know how it goes!
DL_single_mask_pipeline.cpproj (705 KB)