Should I choose Bio7 or Fiji?

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Should I choose Bio7 or Fiji?

Ali Roberts
I'm a cell biologist who mainly needs image analysis and processing for confocal microscope images, plus some other simple analysis of images with biological relevance.  I've used Fiji in the past but have just discovered Bio7.  Which should I choose to download now?  If I install Bio7 and add in the Fiji plugin will I have both sets of plugins and fullest options? Thanks for help and advice.....
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Re: Should I choose Bio7 or Fiji?

Marcel
Bio7 integrates ImageJ as a plugin and some ImageJ2 plugins. You can extend Bio7 with all ImageJ plugins. Special FIJI plugins (based on ImageJ2 libraries) won't work out of the box if not comatible with IJ1.

Here is what I can say about Bio7:

Bio7 is a dynamic programming environment for Java, R, J(P)ython, BeanShell, Groovy, etc...

It has a tight integration of R and ImageJ if you want to combine image analysis data with R statistics,see:

https://www.youtube.com/playlist?list=PLzCgXMp4TBsVKSRHZ8Q9y_3ZSlGl2kcrp

https://www.youtube.com/watch?v=t3OOEZ5sBLY


In addition Bio7 is based on Eclipse and you can extend Bio7 with some Eclipse plugins (advanced editors for Python, JavaScript, etc.). It has also a dynamic Java compiler to test ImageJ plugins on the fly and run them dynamically in the current running Bio7 process.

For the next release (soon to be released) I implemented a even tighter integration of ImageJ added JavaScript support, improved the GUI and also improved the generation of knitr, rmarkdown and LaTeX documents.

For an overview, see my Bio7 channel on Youtube:

https://www.youtube.com/watch?v=pyYn690KaNE

Or consult the Bio7 documentation:

http://bio7.org/manual/Main.html