Year installed: 2020
 
Location: main lab
→ Amira Workstation Usage Statistics

===== 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 RTX2070 - 8 GB VRAM * OS: Windows10 Pro 64 Bits * Data storage: 1TB 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. ---- [[resources|Back to the Equipment page]]