ImageJ Documentation Wiki faq:technical
https://imagejdocu.list.lu/
2026-11-15T23:10:38+00:00ImageJ Documentation Wiki
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https://imagejdocu.list.lu/lib/tpl/dokuwiki/images/favicon.icotext/html2021-04-01T05:13:46+00:00Anonymous (anonymous@undisclosed.example.com)FAQ: Are there performance statistics to compare against my system?
https://imagejdocu.list.lu/faq/technical/are_there_performance_statistics_to_compare_against_my_system?rev=1617246826&do=diff
FAQ: Are there performance statistics to compare against my system?
What is ImageJ's typical performance on various system configurations, and how does my machine compare to them?
ImageJ has a Benchmark utility you can run to evaluate your system's performance.text/html2019-04-12T13:13:41+00:00Anonymous (anonymous@undisclosed.example.com)FAQ: Can I convert a large stack into .avi, .gif, QuickTime without loading it?
https://imagejdocu.list.lu/faq/technical/can_i_convert_a_large_stack_into_.avi_.gif_quicktime_without_loading_it?rev=1555067621&do=diff
FAQ: Can I convert a large stack into .avi, .gif, QuickTime without loading it?
Some stacks are too large to fit in RAM to be loaded and saved in an animation format. How do I overcome this?
Wayne provided this answer in the mailing list:
With ImageJ 1.39k and later, you can frame-by-frame convert a large TIFF by opening stack it usingtext/html2019-04-12T13:13:41+00:00Anonymous (anonymous@undisclosed.example.com)FAQ: How do I get the information from the cursor in the status bar?
https://imagejdocu.list.lu/faq/technical/how_can_i_understand_status_bar_mouse_informations?rev=1555067621&do=diff
FAQ: How do I get the information from the cursor in the status bar?
When dragging the mouse over an image, ImageJ shows some information about the pixel under the mouse cursor.
This can however vary across different plugins.
The information comes from thetext/html2019-04-12T13:13:41+00:00Anonymous (anonymous@undisclosed.example.com)FAQ: How do I increase the memory in ImageJ?
https://imagejdocu.list.lu/faq/technical/how_do_i_increase_the_memory_in_imagej?rev=1555067621&do=diff
FAQ: How do I increase the memory in ImageJ?
Yes, the amount of memory available can be increased, up to a limit. It is not a good idea to increase above 3/4 of the physical memory available, nor should memory be increased on Mac OS 9 or earlier in most cases (but see the Mactext/html2019-04-12T13:13:41+00:00Anonymous (anonymous@undisclosed.example.com)FAQ: How do I quantify a gel with ImageJ ?
https://imagejdocu.list.lu/faq/technical/how_do_i_quantify_a_gel_with_imagej?rev=1555067621&do=diff
FAQ: How do I quantify a gel with ImageJ ?
Electrophoretic gels such as Western blots can be quantified easily with ImageJ using the Analyze▷Gels▷ commands, as described on this video tutorial. Further details are explained on the ImageJ User Guide. Please read the Guide's sectiontext/html2019-04-12T13:13:41+00:00Anonymous (anonymous@undisclosed.example.com)FAQ: How do I run ImageJ without a graphics environment (headless)?
https://imagejdocu.list.lu/faq/technical/how_do_i_run_imagej_without_a_graphics_environment_headless?rev=1555067621&do=diff
FAQ: How do I run ImageJ without a graphics environment (headless)?
I want to run ImageJ on a cluster, by executing batch macros. To do that, I use ssh to log on, but ImageJ throws an exception that it cannot create a Menu in headless mode. What to do?text/html2019-04-12T13:13:41+00:00Anonymous (anonymous@undisclosed.example.com)FAQ: How do I run the garbage collector in a macro or plugin?
https://imagejdocu.list.lu/faq/technical/how_do_i_run_the_garbage_collector_in_a_macro_or_plugin?rev=1555067621&do=diff
FAQ: How do I run the garbage collector in a macro or plugin?
If a macro or plugin runs out of memory, you can force garbage collection.
The Java Virtual Machine does garbage collection automatically as necessary, but this can also be forced at a particular time in a plugin or a macro.text/html2019-04-12T13:13:41+00:00Anonymous (anonymous@undisclosed.example.com)FAQ: How do I set up ImageJ to deal with white particles (on a black background) by default?
https://imagejdocu.list.lu/faq/technical/how_do_i_set_up_imagej_to_deal_with_white_particles_on_a_black_background_by_default?rev=1555067621&do=diff
FAQ: How do I set up ImageJ to deal with white particles (on a black background) by default?
ImageJ can be set to deal with white particles on a black background or black particles on a white background. The latter is the default. How do I change that?text/html2019-04-12T13:13:41+00:00Anonymous (anonymous@undisclosed.example.com)FAQ: How do I update ImageJ?
https://imagejdocu.list.lu/faq/technical/how_do_i_update_imagej?rev=1555067621&do=diff
FAQ: How do I update ImageJ?
Once installed, updating ImageJ consists only of downloading the latest ij.jar file and copying it into the ImageJ folder (this replaces the current file, so make sure that ImageJ is not running and that the file has thetext/html2019-04-12T13:13:41+00:00Anonymous (anonymous@undisclosed.example.com)FAQ: How to find the code behind a given menu command?
https://imagejdocu.list.lu/faq/technical/how_to_find_the_code_behind_a_given_menu_command?rev=1555067621&do=diff
FAQ: How to find the code behind a given menu command?
You can look in the IJ_Props.txt file the exact plugin called by a given menu command.
For example for the 'Make Binary' menu entry, the IJ_Props.txt file reads
binary01="Make Binary",ij.plugin.Thresholdertext/html2019-04-12T13:13:41+00:00Anonymous (anonymous@undisclosed.example.com)FAQ: I need an old version of the ij.jar file. Where can I get it?
https://imagejdocu.list.lu/faq/technical/i_need_an_old_version_of_the_ij.jar_file._where_can_i_get_it?rev=1555067621&do=diff
FAQ: I need an old version of the ij.jar file. Where can I get it?
Given that ImageJ is constantly evolving, sometimes an old plugin may only run with a previous version of ImageJ and not the newest. Where can one get those older ij.jar files?
Thetext/html2019-04-12T13:13:41+00:00Anonymous (anonymous@undisclosed.example.com)FAQ: My image stack is too large!
https://imagejdocu.list.lu/faq/technical/my_image_stack_is_too_large?rev=1555067621&do=diff
FAQ: My image stack is too large!
The image stack I am trying to load is too large for the memory I can allocate. Is there any way I can load it?
You might be able to work around the memory limit by using the Virtual Stack Opener plugin at: <http://rsb.info.nih.gov/ij/plugins/virtual-opener.html> This plugin allows viewing and analyzing image sequences that do not fit in memory.text/html2019-04-12T13:13:41+00:00Anonymous (anonymous@undisclosed.example.com)FAQ: What are the algorithms used to calculate particle area and perimeter?
https://imagejdocu.list.lu/faq/technical/what_are_the_algorithms_used_to_calculate_particle_area_and_perimeter?rev=1555067621&do=diff
FAQ: What are the algorithms used to calculate particle area and perimeter?
The Particle Analyzer calculates Area as the number of pixels forming the 8-neighbour connected particle.
The Perimeter is calculated by the getTracedPerimeter() method in thetext/html2019-04-12T13:13:41+00:00Anonymous (anonymous@undisclosed.example.com)FAQ: What is the algorithm used in automatic thresholding?
https://imagejdocu.list.lu/faq/technical/what_is_the_algorithm_used_in_automatic_thresholding?rev=1555067621&do=diff
FAQ: What is the algorithm used in automatic thresholding?
What is the algorithm used by ImageJ to find the ideal threshold value?
The automatic thresholding function used by Image>Adjust>Threshold and Process>Binary>Threshold is an iterative procedure based on thetext/html2019-04-12T13:13:41+00:00Anonymous (anonymous@undisclosed.example.com)FAQ: What is the algorithm used in Find Edges?
https://imagejdocu.list.lu/faq/technical/what_is_the_algorithm_used_in_find_edges?rev=1555067621&do=diff
FAQ: What is the algorithm used in Find Edges?
It is the 3×3 Sobel edge filter.
The source is in the filter() method of the ij/process/ByteProcessor.java class.
...
case FIND_EDGES: // 3x3 Sobel filter
sum1 = p1 + 2*p2 + p3 - p7 - 2*p8 - p9;
sum2 = p1 + 2*p4 + p7 - p3 - 2*p6 - p9;
sum = (int)Math.sqrt(sum1*sum1 + sum2*sum2);
if (sum> 255) sum = 255;
break;
...