Getting started with macros in ImageJ transcript

hi welcome back to the channel it's been a while because it's been a really busy semester and what i want to do today was to quickly show you how to use macros in mhj i've got a student who's doing a project at the moment and she has a fairly simple but repetitive image analysis image processing routine that you need to work through and i thought probably the quickest thing to do would be to build a macro and then it occurred to me that perhaps this might make a useful youtube video since i haven't made one for probably just over a month now so getting started with macros in mhj let's crack on with it grab your coffee but you actually might not need it because this is going to be a quick one [Music] [Laughter] okay so this is a fairly simple image analysis routine we have a bunch of folders and in each folder we have a data set which is a stack of images there are three images one from channel one channel two and channel three which in this case has no data so what we'll do is we will record a process on this data set and then we will apply it to all of these data sets here one by one all right so first process is to go to macros and let's record what we do okay so there's our record panel here right so i've selected my image and the first thing i will do is go stacks stack to images okay so you see here it runs the stack to images i will close channel 3 because i don't need that one i will run and enhance contrast on image one i'll normalize it okay it looks okay actually i'll select image two and run an enhanced contrast i'm going to make channel one my red channel look up tables and now i'm going to merge these two channels so color merge channels i'll make the red channel channel one the green channel channel two i'll keep the source images no actually i'll lose the source images and click ok boom there we go we have our composite image which i could then save but what i'll do here is i will just create this now so i create my macro and here it is i will give it a name so i'll save it as let's say split and color cd my initials dot image j macro igm and that's important that you give it that ijm name okay so i have created my macro but now i need to put it in the macro folder so here is my macro that i have created and here in imagej in the macros folder this is one i created earlier so let's just delete that this is what i'm after the split in color is the one i just made and i simply drag it into the folder so now my image j folder has a macro called split and color so if we go to our plugins and go macros we can install this macro here is split in color cd we'll open that and now we see if we go to macros that we have the split in color so let's test it let's get a different image load this one in and we'll run the macro there we go get a different one will be one from here select the image and macros and you can see how much time this potentially saves micros so there you go that's a start to making macros a very very simple one but hopefully gives you an idea of the components that are involved in making macros in msg i'll see you next time