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Integration with ImageJ Software

ImageJ is popular free, public domain, image processing and analysis software with large number of processing plugins and active user community. You can run ImageJ macros on Simagis Live server and:
  • Use your favorite ImageJ macros and plugins to analyse images of any size
  • Collaboratively develop, test and use ImageJ macros with your colleagues
  • Use ImageJ macros together with Simagis applications for advanced analysis solutions

How to run ImageJ macro on Simagis Live server#

To use ImageJ for analysis of large images efficiently Simagis Live server runs multiple instances of ImageJ process in parallel on arrays of virtual tiles utilizing available computing cores. Simagis Live Server monitors ImageJ performance and can kill and restart ImageJ process if it stalls, crashes or runs out of memory.

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To Upload Images:#

Upload your images usual way either via simple upload or using Turbo Upload utility for large images and image tile mosaics

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Run Macro:#

  1. Select tab “Settings”
  2. In the field ImageJ Macros: paste your ImageJ macro. Note: You can save, load, export and import your macros. Field Aperture overhang contains the value for image tile overlap to avoid edge effects with some kernel processing functions like blur and others. you don’t need to change this field In most cases
  1. Click Execute Button

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View Results#

  1. Open Image Viewer
  2. Select Layer ImageJ
Now you can annotate, measure and share your images with others, see Project Viewing for details

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Download image clips for off-line analysis#

Once processing is complete, you can Download Images to ImageJ for off-line analysis.

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Important Notes:#

  • Running ImageJ function is possible on dedicated hosting servers (commercial or academic collaborator accounts). For security reasons we cannot allow loading custom code to public hosted servers.
  • You need to have all ImageJ plugins required by your macro installed on server prior to running macros
  • You should build your macros such that your resulting image appears in the active ImageJ window at the end of macro execution.
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