Bioimaging Wiki

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Data will be deleted after: <b>3 months</b>
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&nbsp <br><b>Location</b>: <a href="/facility/bioimaging/lib/exe/fetch.php?media=workstations-location.png">Bartolomeu Dias wing B12</a><br>
&rarr; <a href="/facility/bioimaging/doku.php?id=z3_workstation_usage"><img src="/facility/bioimaging/lib/exe/fetch.php?media=chart_line.png">  Z3 Lightsheet Workstation Usage Statistics</a>
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===== System overview =====
Z3 is a 64-bit PC running Windows 10, equipped with:
  * 2x Intel® Xeon Processor E5.2620 @ 2.4GHz
  * 128 GB DDR4 RAM memory 
  * 2x 256 GB SSD + 36 TB disk space
  * 8 GB NVIDIA Quadro P4000 (graphics card)
  * 28" TFT monitor

===== Software  =====

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

  * {{zen_icon.png?35|}} **[[https://www.zeiss.com/microscopy/en/products/software/zeiss-zen.html|Zeiss ZEN Blue 3.1 Desk]]**
      * **Airyscan Processing**, Stitching and MIP of .CZI files

  * {{zen_black_icon.png?35|}} **[[https://www.zeiss.com/microscopy/en/products/software/zeiss-zen.html|Zeiss ZEN Black 3.1 Desk]]**
      * **Lightsheet Processing**

  * {{:qupath_icon.png?35|}} **[[https://qupath.github.io/|QuPath 0.5.1]]**
      * Open Software for Bioimage Analysis of whole slide images

  * {{:matlab_icon.png?35|}} **[[https://www.mathworks.com/products/matlab.html?s_tid=hp_products_matlab|MATLAB R2024b]]**
      * Programming and numeric computing platform, with the following toolboxes: Curve Fitting, Image Acquisition and Image Processing, Optimization and Parallel Computing, Partial Differential Equation and Statistics and Machine Learning

  * {{:cellprofiler-icon.png?35|}} **[[https://cellprofiler.org/|CellProfiler 4.2.8]]**
      * Open Software for Bioimage Analysis to quantitatively measure phenotypes from thousands of images automatically.

  * {{slidebook_2022_icon.png?35|}} **[[https://www.intelligent-imaging.com/slidebook|3i Slidebook Reader 6]]**
      * Supports .SLD file format.

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

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[[resources|Back to the Equipment page]]
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