Technical help sheet
Technical requirements for data analysis
The practicals in this course were run on virtual machines with Linux Ubuntu 22.04 Operating Systems, 16 GB of RAM, 8 vCPUs, and 200GB of storage capacity.
These were the tools used for executing the practicals in this course:
Image Data resources and Distributed/Cloud computing
| SOFTWARE | URL for software / Software version |
| Git | github.com |
| Web Browser (preferably chrome) (example) | https://www.google.com/chrome |
| Mamba | https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html |
| QuPath (with the OMERO extension) | https://omero-guides.readthedocs.io/en/latest/qupath/docs/installation.html |
| Fiji | https://imagej.net/software/fiji/downloads |
| OMERO plugin for Fiji | https://omero-guides.readthedocs.io/en/latest/fiji/docs/installation.html |
ilaskik
| ilastik | https://www.ilastik.org/download.html#beta Version: 1.4.1b15-gpu (most likely will be updated, what would be the deadline?) |
| webbrowser, preferrably chrome | https://www.google.com/chrome/ |
| nvidia driver (ilastik ships its own cuda) | |
| Fiji | https://imagej.net/software/fiji/downloads |
| ilastik Fiji plugin | https://github.com/ilastik/ilastik4ij?tab=readme-ov-file#installation |
| MoBiE Fiji Plugin | https://github.com/mobie/mobie-viewer-fiji?tab=readme-ov-file#install |
pyThorch introduction and Advanced topics (Terminal, Snakemake, pyTorch)
| conda/mamba |
| Git |
| pytorch |
| cudatoolkit |
| pytorch-lightning |
| snakemake |
| https://pypi.org/project/torchvision/ |
CellProfiller
Ideally Ubuntu 20.04 is required, as the build version has been already tested for this. Once Python 3.8 or 3.9 are installed, it should just be pip install cellprofiler, but it needs one of those python versions, for which we don’t have Ubuntu 22.04 instructions.
| CellProfiler 4.2.6 | https://github.com/CellProfiler/CellProfiler/wiki/Ubuntu-20.04 |
| Workshop materials | https://tutorials.cellprofiler.org/#beginner-segmentation |
BioImage Model Zoo
| Docker (with enough permissions as to download and build new docker images) | https://www.docker.com/products/docker-desktop/ |
| Docker Desktop | |
| DL4MicEverywhere | https://github.com/HenriquesLab/DL4MicEverywhere |
| Google Chrome |