amira
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amira [2025/01/06 01:44] bioimaging created |
amira [2025/01/13 17:14] (current) bioimaging [Software Installed] |
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| - | <a href="/facility/bioimaging/lib/exe/fetch.php?media=amira.png"><img src="/facility/bioimaging/lib/exe/fetch.php?media=chronos.png"></a> | + | <a href="/facility/bioimaging/lib/exe/fetch.php?media=oeiras_-_amira_workstation.png"><img src="/facility/bioimaging/lib/exe/fetch.php?media=oeiras_-_amira_workstation.png"></a> |
| <td style="border:0px solid white;"> <p style="line-height:1.8"> | <td style="border:0px solid white;"> <p style="line-height:1.8"> | ||
|   <br> |   <br> | ||
|   <br> |   <br> | ||
| - |   <br> | + |   <br><b>Year installed</b>: 2020 <br> |
| - |   <br> | + |   <br><b>Location</b>: main lab <br> |
| - |   <br> | + | → <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> |
| - |   <br> | + | |
| - |   <br><b>Location</b>: <a href="/facility/bioimaging/lib/exe/fetch.php?media=colossus_map_new.png">Room P3-A-5</a><br> | + | |
| - | → <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> | + | |
| </p> | </p> | ||
| </td> | </td> | ||
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| ===== System overview ===== | ===== 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 | ||
| - | ===== Software ===== | ||
| + | {{: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]] | [[resources|Back to the Equipment page]] | ||
amira.1736124257.txt.gz · Last modified: 2025/01/06 01:44 by bioimaging
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