I am trying to analyse intracellular prokaryotic pathogens using ICY software protocols with 4-channels max projected tilled large images (2700 px by 3700 px) :
- here is the protocol I made :
icy protocol colox intra dapi contour v5s2v3 120h.protocol (23.3 KB)
The type of image I want to analyse is the following :
The image comes from an LSM700. Originaly .czi format, I save a stiched max projection in tiff that I use as input in ICY.
- Upload an original image file here directly or share via a link to a file-sharing site (such as Dropbox).
- Share a minimal working example of your macro code.
The 4 channels are as follow :
channel 0 : extra cellular prokaryotic cells
channel 1 : eukaryotic cells plasma membrane
channel 2 : DAPI (eukaryotic cells nuclei)
channel 3 : total prokaryotic cells
The protocol allows detection of intracellular prokaryotes using spot detector on channel 0 and 3 then colocalization studio to get channel 3 specific objetcs. hk means detects nuclei to root active contour and get cell edge.
My issue is that even after overnight run, the protocol is stuck at active contour (around 2000 object to analyse). Would you have a way to handle such big files (reslice the images ?).
Have a good day