Replies Created

  • Stephane Dallongeville

    We indeed need to improve the old “intensity profil” plugin to bring support of 3D ROI 🙂

    Stephane Dallongeville

    Note that i specified “path intensity profil” plugin which is different from the “intensity profil” plugin 🙂

    Stephane Dallongeville

    Hello,

    By default indeed it will just export data about the global shape (mean intensity for instance). If you want to have the profil along the line then you can use the Path Intensity Profil plugin (just type its name into the search bar of Icy to access it).
    It will produces you a table (that you can export in XLS) with each points of the line providing coordinates and intensity values:

    Path intensity profil

    Hope that helps !

    – Stephane

    Stephane Dallongeville

    Hello,

    In fact you already have the open recent into the menu :

    Just clicking on the top left icon will show the main menu, and by default it shows the Recent Files but you have it too when you select the Open command. Also by default Icy remembers the last used folder independently for opened / saved files.

    – Stephane

     

    Stephane Dallongeville

    If you had a look in the code, you can understand why it’s not really easy to add this feature, still we will consider it and see the best approach about how implement it without interfering / troubleshooting the current implementation. We will be honest, the feature won’t happen that soon i guess, even if we find a way to do it.

    Best,

    – Stephane

    Stephane Dallongeville

    Hi Frederic,

    There is no way of editing multiple points at the same time. Do you want to move all those selected points in the same way ? To be honest it would be difficult to add that feature given the current implementation / logic about how ROI works (as you can see only 1 point can be “focused” at once).

    I think that would require a specific development but again i hardly see how do it.

    Currently the rectangle selection is already used to select a group of ROI (and not directly the control point). It could be eventually done using Ctrl+Click on control points but we have to see how much this is really possible to integrate it into current implementation, still we will study that possibility.

    – Stephane

     

    Stephane Dallongeville

    Already replied in the other topic and as i said i think it’s better to limit the number of input argument as much as possible. Still adding that kind of constraints could be interesting but if they work not only for entering objects but for everything in general (so we could easily discard / stop tracking of incorrect objects in general).

    We will keep that somewhere in our mind, trying to find a good way to add these constraints without making the GUI looks too complex / overloaded (imo it already looks too complex).

    Stephane Dallongeville

    Hi Deborah,

    The problem is that Active Contour plugin already has many input parameters to say the least ! I think that it’s better to not increase it if possible to not make it more complex than it is already ^^ even more when we can just filter results afterward (this can be done automatically too, with a protocol). If the filtering is working in your case then it’s probably better going that way 🙂

    Best,

    – Stephane

    Stephane Dallongeville

    Thanks ! To be honest there is still many small issues to fix with it but at least i think it’s more appealing than the old site 🙂

    Stephane Dallongeville

    Hi Marine,

    I just set up a small protocol to do it called “Remove ROIS touching image border”.
    You can download it directly from the application typing “Remove ROIS” into the search bar, it should appears in the “Procotol” section of result (at bottom).

    Best,

    – Stephane

    Stephane Dallongeville

    Hi Frederic,

    You can find all the tutorials in the training page :

    Train others & yourself

    Note that links won’t open / download if you try to open them from the page, but if you take the link URL into a new tab then it downloads correctly the PDF file (we will fix this problem asap).

    Best,

    – Stephane

    Stephane Dallongeville

    Hi,

    The only 3D correction drift plugin i see in ImageJ is a python script using ImgLib2 and other dependencies, is this that plugin you were speaking about ?

    In which case so you will need first to install all dependencies in the IJ folder of Icy, then you will probably need to install jython to be able to execute the script right from the Script Editor within Icy (but you should be able to use it from ImageJ as well).

    – Stephane

    Stephane Dallongeville

    Glad you were able to find the solution 🙂

    Stephane Dallongeville

    I guess that you use 2 separates Sequence (and so viewer) or you have many of them which can be from one type or another ? In the second case what you can do is to eventually use a specific mark in the Sequence name (or is its metadata ?) so instead of using the viewer event you directly use the sequence event.

    Here’s how you can store an information in Sequence metadata (persitent with the XML file):

    Node myNode = sequence.getNode(“myPluginMetadata”);

    // set type
    XMLUtil.setElementValue(myNode, “type”, “type1”);

    Then how use it for sequence activation event:

    Icy.getMainInterface().addActiveSequenceListener(new ActiveSequenceListener()
    {
    @Override
    public void sequenceDeactivated(Sequence sequence)
    {
    Node myNode = sequence.getNode(“myPluginMetadata”);

    // get sequence ‘type’
    if (XMLUtil.getElementValue(myNode, “type”, “”).equals(“typeA”))
    // do something
    }

    @Override
    public void sequenceActivated(Sequence sequence)
    {
    Node myNode = sequence.getNode(“myPluginMetadata”);

    // get sequence ‘type’
    if (XMLUtil.getElementValue(myNode, “type”, “”).equals(“typeA”))
    // do something
    }

    @Override
    public void activeSequenceChanged(SequenceEvent event)
    {
    // TODO Auto-generated method stub

    }
    });

    Stephane Dallongeville

    Hi Frederic,

    Icy has that kind of event so you can actually listen them and react to it:

    [/crayon]

    Hope that was what you were looking for.

    Best,

    – Stephane