New to FIJI and ImageJ here, so I apologize if this question sounds idiotic to the veterans. I came across a really cool toolset that can deblur laser scanning microscopy images here: http://image.bio.methods.free.fr/lsmtrans.html but it is missing from my newly downloaded FIJI release. I think I found the code here: http://rsb.info.nih.gov/ij/macros/toolsets/LSM%20Transmission%20Deblurring.txt but I have no idea how to install it by hand. Do I need to save it notepad++ as a .jar (code looks like java) or .ijm file? Or is there a way to search for it from the FIJI application?
My FIJI version: ImageJ 1.52p Java 1.8.0_172 (64 bit)
To manually install a Toolset:
Save a local copy of the file (txt extension)
Navigate to Macros/Toolsets inside your Fiji installation (on a Mac, access this by right clicking on the Fiji app in a Finder window and selecting "Show Package Contents")
Copy the file to this location
Restart Fiji if it was running
Toolset is available by clicking >> in the toolbar
Related
I'm trying to use the ESRF edf plugins for ImageJ with Fiji as I also need to open 64-bit TIFF files which I cannot with ImageJ - Unsupported format or file not found.
https://www.esrf.fr/UsersAndScience/Experiments/Imaging/ID19/Software/slice-by-slice-volume-opener
https://github.com/olofsvensson/esrf-imagej-plugins/tree/master/ESRFPlugins/plugins
I have an old version of Fiji (https://github.com/Nin17/ImageJ-FIJI/tree/main) that works with the edf plugins but cannot open 64-bit TIFF files.
Unsupported bits per sample 64: https://i.stack.imgur.com/UARtZ.png
If I update Fiji to accept the 64-bit TIFFs it can no longer accept the edf files if I set them to open with Fiji or in drag and drop - it says 'Initialising base reader' and then produces something like this:
Incorrectly opened edf file: https://i.stack.imgur.com/3d02o.jpg
I can still open the edf files if I go to Plugins -> Input-Ouput -> EDFRead but this is time consuming if I have to open lots of edf files.
If I put the edf plugin files present in my old version of Fiji into a recently downloaded Fiji I get the same result.
I've tried comparing files between the two versions but I have no knowledge of Java so I don't really know what I'm looking for.
In short, how do I use the ESRF edf plugins with a single version of Fiji that can open both .edf and 64-bit tiff in either drag and drop or open with.
Apologies in advance for the dated software question:
According to Code Composer help documentation the "Memory Load/Save Utility" should be be in the Tools menu. In my Code Composer 3.3 (which I have to use for this project, so I cannot upgrade), does not have this option in the tools menu, or any menu that I could find. It is not greyed out - it is just simply missing as far as I can tell. I've changed every view option to try and enable this.
Can anyone help me figure out how to enable/activate this option? Does the processor need to be in a specific state? Is this a special plug-in that I can't find?
Here is my setup:
Code Composer 3.3, Windows Xp, Using a Spectrum Digital xds510pp JTAG emulator on a TI ARM 9 processor.
Specifically the option is here: 13. Memory Load/Save Utility:
http://www.ti.com/lit/an/spraa07c/spraa07c.pdf
[EDIT] The File > Data > Save - this is not the same as the Memory Load/Save Utility. This sounds similar but does not export the values.
For example, I need to export data at a certain memory address for a certain length into a hex format.
Somehow my installation went bad.
I checked the Code Composer Studio Component Manager by running C:\CodeComposer3.3\cc\bin\comp_mgr.exe. Now, in this window un the TI node, there should be numerous plugins and one of which should be: "Memory Save/Load Utility Control..."
For me this was missing.
Repairing the installation via windows control panel did not work. I had to uninstall and then reinstalled. Upon reinstalling a TMS470 driver was reported missing. Not sure why this was.
Again, I uninstalled then complete removed the C:\CodeComposer3.3\ directory, then reinstalled. This time everything seemed to have worked and I do have the Memory Save/Load Utility and it is working.
EDIT:
It should also be noted that the plugins are bundled with the installer and could not be re installed separately.
I need to add a toolbox to my Matlab Student version. I know that I have to download the toolbox files, place them in some directory and then specify a path.
However, I am not quite sure about where I have to place my files.
I downloaded two zip archives: 'Symbolic Math Toolbox (Common) 5.10' and 'Symbolic Math Toolbox 5.10'.
Where do I have to place them on Mac OSX Mountain Lion?
How and where do I specifiy the path?
Thank you all, this will help me a lot with my project!
Ok, I figured it out: Here what you do on Mac OS X Mountain Lion:
Downloading the files/ toolbox:
Login to your MatWorks account.
Click on your name in the upper right corner.
Go to 'Manage Licenses' in the 'My Licenses' section on the left.
Click on 'Download products'
Select your Operating System (in this case Mac OS X)
Choose the option 'Choose products and versions to download for the platform(s) selected.' and click continue.
Select the toolboxes that you want and click continue.
A small window will pop up. Since you already have Matlab installed you don't want to tick Matlab. Just click continue.
Since I didn't get the automatic installer working I used the manual download. Click on 'try manual download.'
Download the installer, and the remaining files (2 per toolbox)
Now that you have downloaded everything we can continue with the installation.
Installing the toolbox:
Unzip the installer file (if it did not unzip automatically).
Place the ZIP FILES (IMPORTANT) of your toolbox inside the installer directory.
Double click the installer and follow the the instructions.
NOTE:
You might have to enter a file activation key. You can redownload it from the 'Manage License' page (the one we visited at the beginning) under the 'Activation and Installation' tab. There just click on 'Get license file' and you can download the license file and copy the file activation key.
Hope this is helpful to anyone! If so, give it a vote!
cheers!
I am trying to install opencv in windows. The manual (secn 1.4) says "choose a build [e.g. vs2010, win32] and download", but there is only the full executable file available (for 2.4.2). So I downloaded that file, which then expanded into several directories. However, this directory list does not match what is shown under item 7 of the section - mainly the "bin" directory is missing. So I guess something more has to be done besides just clicking on the executable.
Under "build" dir, I see x86/vc10/bin (I am guessing that vc10 stands for visual c++ 2010). But how do I install these and link visual studio 2010 with it? The manual only says to setup "OPENCV_DIR" variable which should have "bin" under it, but I dont have that.
This seems like a real problem any new user would face with opencv installation. Any correct instructions and link available on how to install for windows+visual studio 2010?
Updates: Full solution posted below.
After much experimentation, I have got opencv-2.4.2(win-exe) + vstudio2010-express working together. Thanks to Abid, for providing a helpful link, an additional helpful link is http://blog.hcilab.org/bastian/2012/06/installing-opencv-2-4-windows-7-visual-studio
Here is the full list of steps:
set system var OPENCV_DIR = install_dir\build
set system var TBBROOT = tbb_install_dir
path += ;%OPENCV_DIR%\x86\vc10\bin;%TBBROOT%\bin\ia32\vc10
create empty project: File->New->Project->Win32ConsoleApp
add the following items in project->Properties:
ConfigProperties->VC++Dirs->Include: $(OPENCV_DIR)\include;$(TBBROOT)\include
Linker->General->AdditionalLibDirs: $(OPENCV_DIR)\x86\vc10\lib;$(TBBROOT)\lib\ia32\vc10
Linker->Input->AdditionalDeps: add lib items from opencv and tbb (in Debug and Release modes).
for details of which files to include, see http://docs.opencv.org/doc/tutorials/introduction/windows_visual_studio_Opencv/windows_visual_studio_Opencv.html#windows-visual-studio-how-to
download image-display test file from above site, save it in the project dir. But the Test.cpp in that page requires more inputs, so it does not work easily. Instead, use the code from http://docs.opencv.org/doc/tutorials/introduction/display_image/display_image.html#display-image
Properties->ConfigProps->Debugging->CommandArgs: mention file name to be loaded
Tools->Option->Debugging->Symbol->MS-Server=yes (this removes most of the "PDB not found" errors)
Tools->Settings->ExpertSettings=on (this also removes some errors)
copy tbb_debug.dll and tbb.dll from TBBROOT\bin\ia32\vc10 to the project dir (I dont know why these are not automatically picked up with the settings done above)
Ctrl+F5 to run (start without debugging)
i think your installation is OK. just need to configure with VS
in Project Properties > C/C++ >
Add Additional Include Directory: C:\opencv\build\include;C:\opencv\build\include\opencv
C/C++ > Linker > Input add Additional Dependencies :
C:\opencv\build\x86\vc9\lib\opencv_core231.lib
C:\opencv\build\x86\vc9\lib\opencv_flann231.lib
C:\opencv\build\x86\vc9\lib\opencv_highgui231.lib
C:\opencv\build\x86\vc9\lib\opencv_imgproc231.lib
and more if needed
add OPENCV_DIR environment variable with value C:\opencv\build\x86\vc10\bin
more detail follow this OpenCV 2.1 with MS Visual Studio
I want to write some short numerical programs in chapel. Can somebody just tell an IDE, or text editor which supports code highlighting for chapel (chapel-aware), is there an elisp-file for emacs? I don't prefer vim, even if a script for vim exists.
I tried searching, but I couldn't find anything. I neither know emacs-lisp nor am completely aware of chapel's syntax to configure it to make this chapel-aware.
the elisp files and .vimrc files ship along with chapel tar.gz file , so after extracting the tar.gz file in a folder chapel-version/highlight/vim or chapel-version/highlight/emacs there the vimrc or elisp files are present and in the README , instructions are also given how to add to init files ~/.emacs or ~/.vim.
I have just come across a plugin for the Atom Editor that does Chapel Highlighting
There is an Emacs mode for Chapel at MELPA. So if you are using an Emacs with package management you can just install chapel-mode.
https://melpa.org/#/chapel-mode