Software made and used by the lab.
New lab member UU-specific IT instructions to setup: 🛜eduroam 👩🏼💻software licenses.
🌍Travel booking software ✈️. 💾NAS. 🧬TubSeq Sanger 🖨️Poster printing
Microscopes
We have a Nikon Spinning Disc Confocal (SDC) with the following specs (FPbase.org link to light source, filters and detector specs):
Maintainer
We maintain the follow software.
| Software name | Used for | Language | OS | Need support? |
|---|---|---|---|---|
| WholeBrain | whole brain reconstruction, segmentation, atlas registration | ++ | macOS, Linux, Windows | login on gitter chat |
| µLRM | local run manager for in situ sequencing | ++ | macOS, Linux, Windows | |
| furthlab_chem | drawing chemical structures online | macOS, Linux, Windows |
User
These are software that all lab members use inorder to write, communicate and share their work with each other.
Also visit: medarbetarportalen (MP) at UU to install software provided by Uppsala University (Word, PowerPoint etc.).
| Software name | Used for | Alternative | OS |
|---|---|---|---|
| Affinity Designer | Vector graphics/publication quality figures. Good on the iPad. | Adobe Illustrator | macOS, Windows, iOS |
 Element |
Team communication | Slack | macOS, Windows, Linux, iOS, Android |
| GoogleDocs | General writing | Microsoft Word | Cloud |
| GoogleDrive | Collaborative document/file management | Cloud | |
| GitHub | Software maintainance | Git | |
| Quarto | Typesetting (LaTeX) and dynamic content with Python, R, Julia, and Observable. | OverLeaf | macOS, Linux, Windows |
| Zotero | Reference manager | EndNote, Mendeley | macOS, Windows |
| ChemDrawJS | Chemical structure drawings | ChemDraw | Cloud |
| FreeCAD | computer-aided design and drafting | Blender | macOS, Linux, Windows |
Templates
Alternative to BioRender: open source bioicons.com or NIH-funded bioart.niaid.nih.gov
| Template | Purpose | Used with | GitHub link | Download |
|---|---|---|---|---|
| Dynamic presentation | Template to make dynamic presentations with Reveal.js through markdown with Quarto. | JS | /furthlab/quarto_furthlab_template | |
| SciLifeLab logo | logo of SciLifeLab in format. | Affinity | TBA | TBA |
| Uppsala University logo | logo of UU in format. | Affinity | TBA | TBA |
Video tutorials
NAS for microscope storage and VPN access.