GIMM Bioimaging Wiki

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Processing Data will be deleted after: <b>1 month</b> <br>
Storage 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=colossus_map_new.png">Room P3-A-5</a><br> 
&rarr; <a href="/facility/bioimaging/doku.php?id=chronos_usage"><img src="/facility/bioimaging/lib/exe/fetch.php?media=chart_line.png">  Chronos Usage Statistics</a>
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===== System overview =====
Chronos is a 64-bit PC running Windows 10, equipped with:
  * 2x Intel EMR 6534 2P 8C Processors @ 3.9GHz
  * 256 Gb RAM memory
  * System disk: 960GB Samsung PM9A3 NVMe PCIe
  * Data Storage: 7 Tb
  * Data Processing: 7 Tb (2x Samsung PM893 3.84 TB SATA 6Gb/s as RAID 0)
  * Nvidia RTX4000 ADA Gen 20GB, CUDA capable (graphic card)
  * 26" TFT monitor

Please [[imm-bioimaging@medicina.ulisboa.pt|contact us]] if you wish to use the workstation remotely.

===== Software  =====

  * {{::cell_profiler.png?35|}} **[[https://cellprofiler.org/|CellProfiler 4.2.8]]**
      * Free, open-source software for quantitative analysis of biological images

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

  * {{:imaris_icon.png?35|}}  **[[https://imaris.oxinst.com/|Imaris 10.2.0 CF]]**
      * Visualization, analysis and processing of 3D and 4D microscopy datasets

  * {{:living_image_icon.png?30}}  **[[https://www.revvity.com/category/in-vivo-imaging-software|Living Image 4.8.4]]**
      * Analysis of data acquired in IVIS Lumina LT

  * {{::ndpview_icon.png?35|}} **[[https://www.hamamatsu.com/eu/en/product/life-science-and-medical-systems/digital-slide-scanner/U12388-01.html|NDP.View 2]]**
      * Supports .NDPI file format

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

  * {{:qupath_icon.png?40|}} **[[https://qupath.github.io/|QuPath 0.6.0]]**
      * Open Software for Bioimage Analysis of whole slide images

  * {{slidebook_2022_icon.png?35|}} **[[https://www.intelligent-imaging.com/slidebook|Slidebook Reader 2025]]**
      * Supports .SLD file format.

  * {{zen_icon.png?35|}} **[[https://www.zeiss.com/microscopy/en/products/software/zeiss-zen.html|ZEN Blue 3.12 Desk]]**
      * **Airyscan Processing**, Stitching and MIP of .CZI files

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

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