Hi I have 430 files i need to analyse which are in a folder tree
The plugin i am using is this one: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Intensity_Ratio_Nuclei_Cytoplasm_Tool
the files before being analysed need to be converted to 16 bit greyscale image, then a specific threshold applied on some of them (all have the same file start name eg, DAPI.tif, DAPI 2.tif)
Then each DAPI X.tif turned into a mask and analysed using the plugin is analysed with two other files (TRITC X.tif and FITC X.tif) then the results saved.
What is the best way to do this, as it would take me several hours to do this manually?
Btw I am a beginner when it comes to imageJ so detailed instructions would be useful.
Thanks guys
Please take a look at this page of the ImageJ wiki:
https://imagej.net/Batch
Related
I have PSD file with layer text, I try to modify a layer text in Gimp but I can't find a way to select that text and change it to something else.
Thanks for your help!
Sorry - GIMP stable does not import the text information for PSD files - which means all it "sees" is pixels.
A little bit over 10 years ago, Adobe completely closed the informations about the PSD file format, and the import/export for this format in GIMP stopped evolving. Some 2-3 years ago, the file format started being documented again - but GIMP is a developer-starved project, with few people working on it, everyone as volunteers. Last year, with the Google Summer of Code project, there was some development in the PSD plug-in, and there is some advances
incorporated into the development version of GIMP.
Looking from 10000 meters, it looks like there is logic in place to open the text layers preserving the text information on the new code. I can't be sure because I have no PSD file to test it here.
If,as a workaround, you want to findout the typeface names inside the PSD files, in the past I made a simple Python script to print just that - then it is at least possible to recreate the same layer again inside GIMP: https://github.com/jsbueno/psd_print_resources
I am trying to develop a project that involves fingerprint matching. Now, I am stuck at the stage of Fingerprint thinning. I am coding my project using OpenCV and c++ Visual Studio 2010.
I tried erode() function, but it doesn't preserve the continuity of ridge lines. I also tried the following algorithm of Zhang-Suen thinning,
http://opencv-code.com/quick-tips/implementation-of-thinning-algorithm-in-opencv/
but, this shows an exception at memory location. I don't know how to proceed and i am stuck with this step.
Kindly help me with the code for fingerprint thinning + also preserving continuity of ridges.
If you're just looking for a code example of extraction, SourceAFIS (BSD License) goes from full greyscale to binarized and thinned with some artifact trimming as well and then identifies minutia. It's written in c# but it might give you some bright ideas.
I need some command-line tool to create dds (dxt5 format) from two .png files -- one with rgb channels and one with alpha. It's because I have a waste amount of images to process -- I can't do it manually. It's no problem for me to create script for generating batch file to process all images one by one, but I need tool to create dds from two png-s.
Anyone known such command-line tool ?
Thanks.
P.S. nvDXT.exe is very good but it can't combine rgb and alpha from different files.
If you have Photoshop, you could always use Batch Script (see Batch Scripting Tutorial for an example) to merge the channels (with NVidea plug in installed, you could probably even do the DDS conversion too). Just a thought.
I need to extract the biggest (area) rectangle which contains no transparent pixels from a picture.
Here's an exemple (maybe this hand made solution is wrong though):
I find some link about principles (in python) or same topic related issue (here) but without any answer.
Is it possible to make it with Imagemagick? or any command-line tool on linux?
I didn't find a command-line based tool to do that, so I 'forked' the version proposed by zed (J.F. Sebastian here) on github : largest_rectangle script by zed.
I am using ImageMagick from Commandline in .Net? Although a .Net wrapper (ImageMagick.Net in codeplex) is available but it is still in alpha and does not have implementation for all the command line options e.g Distort, Montage. Therefore I am using System.Diagnostics.Process class to invoke the ImageMagick command line.
What are the Pros/Con of this approach? I can see a performance issue if I have to perform multiple transformation on the same image and if I invoke the command twice then the commandline will load the Image twice. Is there a way I can chain the commands so that output of the first transformation is feed into the second command?
It will definitely be slower, and when you chain commands, you are going to be encoding and decoding the image into a format unnecessarily -- if you do this, make sure you use a lossless format like PNG for intermediate formats. To speed it up, use one without compression.
Two other choices
Use ImageMagick.NET and then wrap anything else you need from imagemagick yourself, probably by contributing to the project
My company, Atalasoft, has a free .NET imaging SDK with a lot of overlap with ImageMagick. You can download here: http://atalasoft.com/photofree -- Montage is basically the same as our Overlay commands and Distort is a 2D transformation, which are all included. If ImageMagick.NET can accept and produce .NET Bitmap objects, then you can use both together fairly easily.