Veryyyy basics of using protocols

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    Isq June 27, 2019 at 12:03 pm

    Hey

    Thanks for a great software, and for all the help I received of my previous questions a few months ago, you guys rock!

    I think I’ll be using Icy a lot, so I want to start making my own protocols but I can’t figure out how to even run the protocol on an image.. But before we get to that:

    Is there a list of the names of the blocks associated with each command a user might want to perform? For example to change the pixel size and time interval, you have to go to Get Metadata -> Set Resolution -> Save metadata, which, although it makes perfect sense now that I know that, I might have not figured out if there wasn’t a protocol already in place for this.

    Before that though, I want to do a z/t conversion to the image sequence/video, which I figured must be the Convert stack block, but again I am not sure. In order to test the protocol on a single image, I just opened my video in Icy, pressed Run on the protocol I created and I got the error that it can’t find the input sequence (yesterday when I did the same, it said the protocol was executed but it didn’t seem to actually perform any tasks on the image).

    I found some tutorials online but the video/screenshots didn’t exist anymore, and several web pages which have also been taken out, so I am lost as to what to do. Maybe there is another tutorial page which I can’t find?

    Thanks in advance!

    PS: I wanted to upload an image of the protocol and the error message but I can’t find how to do attach images in this forum, just URL?

    Stephane Dallongeville July 1, 2019 at 12:09 pm

    Hello,

    First, thanks for the really kind comments you made about Icy 🙂 Glad you appreciate it !

    Unfortunately there is no list of available blocks. Well in fact you do have a list from the menu (when you right click in the protocol workspace area) but it isn’t really well organized. The best way to learn is to look existing protocols (that you can reach from the search bar) and see how they do some specific operations.

    Also you have a basic Protocols tutorial here (available from Get Involded –> Train), you need to open the link in a new page / tab to get it top open :
    https://icy.bioimageanalysis.org/doc/icy-protocols.pdf

    About Z/T conversion, you have the convert stack block, note that by default block work on input image, be sure to use Active Sequence so it will use current active / focused image :

    To insert image on the forum, you can use the image insertion button from the toolbar :

    Hope you will be able to do what you want !

    Best,

    – Stephane

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