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    ChrisWeisiger
    @ChrisWeisiger
    @ctrueden I didn't know that, no. One of the things on our extensive to-do list is to revisit our scripting system.
    It'd be great if we supported more (and better) languages than Beanshell.
    It has a main method which launches it on the CLI.
    And there is a new intepreter GUI written in Swing which uses it, too. You can test it using this class, or in ImageJ2 itself by pressing shift+[.
    Curtis Rueden
    @ctrueden
    It would be great if people like yourself helped to make it a truly useful cross-application thing, instead of just "ImageJ's REPL"
    Curtis Rueden
    @ctrueden
    I should note that the GUI REPL fails to work well with some languages (Clojure, Jython, R and Scala are not working yet for various reasons). Groovy works well though!
    Stefan Helfrich
    @stelfrich
    @ctrueden: I couldn’t figure out a build environment that worked for me. Cygwin and MinGW failed even with some hours of trying. I’ll try again tomorrow..
    ChrisWeisiger
    @ChrisWeisiger
    @ctrueden Thanks for the info! Noting it down now for when we get a chance to work on this...
    renfang2016
    @renfang2016
    Hello, there, I have an Image J question, anybody can help please?
    Curtis Rueden
    @ctrueden
    @renfang2016 Feel free to go ahead.
    renfang2016
    @renfang2016
    I am trying to save a sequential numbers of images to one fine at BMP format, but the software I used did not read all the images numbers. It only shows one image number.
    @ctrueden
    Curtis Rueden
    @ctrueden
    Note also that there is an ImageJ Forum with many more people available to help you.
    renfang2016
    @renfang2016
    I am trying to save a sequential numbers of images to one fine at BMP format, but the software I used did not read all the images numbers. It only shows one image number.
    Curtis Rueden
    @ctrueden
    You are trying to save multiple image planes into a single BMP? The BMP format does not support that.
    renfang2016
    @renfang2016
    yes
    Curtis Rueden
    @ctrueden
    You can only save a single image plane to BMP. Try saving as TIFF or perhaps APNG.
    renfang2016
    @renfang2016
    Tree surveyer did not support other format except for BMP
    Curtis Rueden
    @ctrueden
    Is this Tree Surveyer software available for download online?
    renfang2016
    @renfang2016
    I upload the TIFF file to Image J and try to save as BMP. The TIFF file have multiple planes. It showed the BMP file has all the images in Image J though.
    not for free now. It used to be.
    Curtis Rueden
    @ctrueden
    If you need to import multiple image planes into this program, you will need to either: 1) save each file to a separate BMP file, then import them one at a time (or en masse somehow); or 2) save to a multi-plane format which it supports, if any.
    renfang2016
    @renfang2016
    I am at New Orleans Tulane University. Anyone here who is in this city?
    Curtis Rueden
    @ctrueden
    @renfang2016 Regarding New Orleans: not to my knowledge.
    Regarding BMP: I cannot reproduce that success in my ImageJ. File > Open Samples > MRI Stack, then File > Save As > BMP. Then File > Open that file I saved. And there is only one plane.
    renfang2016
    @renfang2016
    In their memo, it is one BMP file and the numbers shows up automatically
    Curtis Rueden
    @ctrueden
    Is this memo somewhere accessible for me to read? Otherwise, I fear I cannot help...
    It sounds like you will have to write to the authors of that software for help.
    But trust me: BMP is single-plane-only.
    renfang2016
    @renfang2016
    Yes, I can send you the link or the manue
    Can you wait a shortwhile and let me find the link to send it to you please?
    Curtis Rueden
    @ctrueden
    If you like.
    Curtis Rueden
    @ctrueden
    @renfang2016 Out of curiosity: have you tried TrackMate? From my outsider's perspective, it looks like it might help you accomplish some of the same things.
    renfang2016
    @renfang2016
    similar to tree surveyor?
    Never heard trackmate
    Curtis Rueden
    @ctrueden
    Well... it's for tracking structures. Fiji also has skeletonization plugins and a Simple Neurite Tracer which can trace things besides neurites.
    Anyway, I cannot find this Tree Surveyor thing anywhere. Just mentioned in that paper, and in a book chapter.
    renfang2016
    @renfang2016
    It is common used software in the kidney development and not many people use it and most people are in Austrilia.
    australia
    Curtis Rueden
    @ctrueden
    You will find people here highly biased toward open-source software. I really cannot help you with closed-source software which we didn't develop here in this chat room.
    Did the authors of Tree Surveyor ignore your questions? Do they provide any support for it?
    renfang2016
    @renfang2016
    Thank you so much for your time.
    Curtis Rueden
    @ctrueden
    I searched that paper you linked but didn't find any mention of BMP files.
    renfang2016
    @renfang2016
    I asked him through e-mail.
    Curtis Rueden
    @ctrueden
    I hope you get a reply! If not, and you are interested in pursuing an open-science-focused solution to your analysis issues, please feel welcome to post on http://forum.imagej.net/ describing your scientific problem, and hopefully some people there can advise you!
    renfang2016
    @renfang2016
    Thank you.
    Curtis Rueden
    @ctrueden
    You're welcome.
    Mark Hiner
    @hinerm
    @ctrueden do you know scijava/scijava-common#239offhand?