GIMM Bioimaging Wiki

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&nbsp <br><b>Year installed</b>: 2020 <br>
&nbsp <br><b>Location</b>: main lab <br> 
&rarr; <a href="/facility/bioimaging/doku.php?id=amira_usage"><img src="/facility/bioimaging/lib/exe/fetch.php?media=chart_line.png">  Amira Workstation Usage Statistics</a>
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===== System overview =====

This workstation has Amira v2020 for 3D image processing and analysis and the Gen5 software (for processing+analysing Cytation5 datasets). It can also be booked for processing demanding FIJI, QuPath and Ilastik operations, and other open-source tools (eg, AI/ML workflows).
If you are not familiar with Amira you can find excellent tutorials here: [[https://www.youtube.com/playlist?list=PLoxdPzacxPYjDVMD4tPCaVbuQjxYizr_g]]

===== Workstation specs (2025)  =====

  * CPU: Intel i9 9900X (10x2 cores) @3.5GHz (max 4.4GHz)
  * RAM: 128 GB DDR4
  * Graphics: nVidia GeForce RTX3060 - 12 GB VRAM
  * OS: Windows10 Pro 64 Bits
  * Data storage: 2TB SSD + 8Tb HHD (both temp space only!)
     => Data is automatically deleted after 3 months of inactivity!


===== Software Installed =====

  * {{:amira_icon.png?35|}} **[[https://www.thermofisher.com/pt/en/home/electron-microscopy/products/software-em-3d-vis/amira-software.html|AMIRA]]**
      * Amira v2020; SOFTWARE FOR 2D-5D MICROSCOPY IMAGE VISUALIZATION AND ANALYSIS

  * {{:gen5_icon.png?35|}} **[[https://www.agilent.com/en/product/cell-analysis/cell-imaging-microscopy/cell-imaging-microscopy-software/biotek-gen5-software-for-imaging-microscopy-1623226|Gen5]]**
      * BioTek Gen5 Software for Imaging & Microscopy

  * {{:fiji_icon.png?35|}} **[[https://imagej.net/software/fiji/|FIJI]]**
      * FIJI is just ImageJ (“batteries-included” distribution of ImageJ2)

  * {{:qupath_icon.png?40|}} **[[https://qupath.github.io/|QuPath 0.4.3]]**
      * Open Software for Bioimage Analysis of whole slide images

  * {{zen_icon.png?35|}} **[[https://www.zeiss.com/microscopy/en/products/software/zeiss-zen.html|Zeiss ZEN Blue 3.3 Desk]]**
      * **Airyscan Processing**, Stitching and MIP of .CZI files

  * {{slidebook_2022_icon.png?35|}} **[[https://www.intelligent-imaging.com/slidebook|3i Slidebook Reader 2022]]**
      * Supports .SLD file format.

  * {{nis_icon.png?35|}} **[[https://www.microscope.healthcare.nikon.com/products/software/nis-elements/viewer|Nikon NIS-Elements Viewer 5.21]]**
      * Supports .ND2 file format


{{:warning.png?25|}} Data files older than **3 months** will be automatically deleted on this system, please copy your data to the server using the desktop link.

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