Difference between revisions of "Fiji/Unet 2016"
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== Introduction == | == Introduction == | ||
U-Net is a plugin for [https://imagej.nih.gov/ij/ ImageJ]. It is a generic deep-learning solution for frequently occurring quantificationtasks like cell detection and shape measurements in biomedical image data. In this case, Unet is built on [https://fiji.sc/ Fiji], a distribution for ImageJ, specifically build to facilitate scientific image analysis. | U-Net is a plugin for [https://imagej.nih.gov/ij/ ImageJ]. It is a generic deep-learning solution for frequently occurring quantificationtasks like cell detection and shape measurements in biomedical image data. In this case, Unet is built on [https://fiji.sc/ Fiji], a distribution for ImageJ, specifically build to facilitate scientific image analysis.[https://lmb.informatik.uni-freiburg.de/Publications/2019/FMBCAMBBR19/paper-U-Net.pdf ¹ ] <br/> | ||
Unet works with and is dependent of a modified version of [https://github.com/BVLC/caffe caffe]: [https://github.com/lmb-freiburg/Unet-Segmentation/wiki/Installation#UNet_Client_Fiji_Plugin caffe_unet]. | Unet works with and is dependent of a modified version of [https://github.com/BVLC/caffe caffe]: [https://github.com/lmb-freiburg/Unet-Segmentation/wiki/Installation#UNet_Client_Fiji_Plugin caffe_unet]. | ||
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== Installed version(s) == | == Installed version(s) == | ||
This version is installed and currently available on environment ''hpc-env | This version is installed and currently available on environment ''hpc-uniol-env'': | ||
caffe_unet/99bd99795d-intel-2016b-Python-2.7.12 | |||
== Using Fiji/Unet == | |||
= | To use Fiji, you need to have a bash session enabled which forwards X11, especially if you depend on the programs GUI. (For more about this you can consult our [https://wiki.hpcuser.uni-oldenburg.de/index.php?title=Login login manual]) | ||
If you want to | If you just want to work with Fiji without GPU support, you can load the module and straight ahead start the program: | ||
module load hpc-uniol-env | |||
module load fiji | |||
fiji-linux64 | |||
Should you need to work with GPUs, you will have to do some preparations: | |||
Revision as of 10:48, 17 September 2019
Introduction
U-Net is a plugin for ImageJ. It is a generic deep-learning solution for frequently occurring quantificationtasks like cell detection and shape measurements in biomedical image data. In this case, Unet is built on Fiji, a distribution for ImageJ, specifically build to facilitate scientific image analysis.¹
Unet works with and is dependent of a modified version of caffe: caffe_unet.
Installed version(s)
This version is installed and currently available on environment hpc-uniol-env:
caffe_unet/99bd99795d-intel-2016b-Python-2.7.12
Using Fiji/Unet
To use Fiji, you need to have a bash session enabled which forwards X11, especially if you depend on the programs GUI. (For more about this you can consult our login manual)
If you just want to work with Fiji without GPU support, you can load the module and straight ahead start the program:
module load hpc-uniol-env module load fiji fiji-linux64
Should you need to work with GPUs, you will have to do some preparations:
Documentation
The full documentation can be found [ here].
