- Step 1 Ordering and opening the images
We use the plugin Bio-Formats Macro Extensions to be able to open only the images we want to treat, saving time and space. To know exactly which ones, primary knowledge of the file architecture is necessary .
As we want to work on all the series of the data, we need to retrieve the number of series. We name the variable seriesCount. Then we will open only the images using a "for loop" selecting the series using Ext.setSeries(i) and opening the right channel with Ext.openImage("title", x). Where is x is the index of the desired channel. 0, the first channel for the dextran and 2, the third channel for the membrane.
Then we run Images to Stack for each channel ordeing them in two separate multitiff images stack, one called DextranChannel and the second one MembraneChannel.
Image to Stack operation lost the scaling factor. We restate it with the function "Set Scale..."