diff --git a/README.md b/README.md index a8a990bd123b44fd74169e9698d349e4d5d57402..524dd8e0529f2177b64005180de5484cd8407cf4 100644 --- a/README.md +++ b/README.md @@ -1,92 +1,150 @@ -# Rat MRI + LS +# Multi-Modal Rat MRI + Light Sheet Brain Dataset -Test +## Short description -## Getting started +Anatomical magnet resonance (MR) brain scans with corresponding whole-brain +Light Sheet images of four wild type rats -To make it easy for you to get started with GitLab, here's a list of recommended next steps. +## Authors -Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)! +* Fahmida Akter (Experiment planning and setup) +* Torsten Stöter (Data curation, Open Data publication) +* Patricia Wenk (Experimentation, MRI acquisition, data curation and analysis) +* Eike Budinger (Supervision, surgery, tissue clearing, Light Sheet imaging, funding, PI) -## Add your files +all affiliated with Combinatorial NeuroImaging Core Facility at Leibniz +Institute for Neurobiology Magdeburg, Germany -- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files -- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command: +## Funding -``` -cd existing_repo -git remote add origin https://git.nfdi4plants.org/torsten.stoeter/rat-mri-ls.git -git branch -M main -git push -uf origin main -``` - -## Integrate with your tools - -- [ ] [Set up project integrations](https://git.nfdi4plants.org/torsten.stoeter/rat-mri-ls/-/settings/integrations) - -## Collaborate with your team - -- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/) -- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html) -- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically) -- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/) -- [ ] [Automatically merge when pipeline succeeds](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html) - -## Test and Deploy - -Use the built-in continuous integration in GitLab. - -- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html) -- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/) -- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html) -- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/) -- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html) - -*** - -# Editing this README - -When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template. - -## Suggestions for a good README -Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information. +CBBS NeuroNetwerk 15 "Non-Invasive Deep Brain Stimulation for Motor Disorders +(NeeMo)" (Budinger, Carius, Ruhnau). +See http://www.cbbs.eu/en/research-funding/neuronetworks/nn15 for details. -## Name -Choose a self-explaining name for your project. - -## Description -Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors. - -## Badges -On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge. - -## Visuals -Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method. - -## Installation -Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection. - -## Usage -Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README. - -## Support -Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc. - -## Roadmap -If you have ideas for releases in the future, it is a good idea to list them in the README. - -## Contributing -State if you are open to contributions and what your requirements are for accepting them. - -For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self. +## License -You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser. +This dataset is made available under the CC-BY-NC-SA 4.0 license. See +https://creativecommons.org/licenses/by-nc-sa/4.0 for details. + +## Data collection + +MRI scans were recorded in mid September 2022, tissue clearing was performed in +March 2023 and Light Sheet images were acquired in early April 2023 at the +Combinatorial NeuroImaging Core Facility of the Leibniz Institute for +Neurobiology Magdeburg, Germany. + +### Rat model + +Wistar Han rat (WT), male, 16 weeks old + +### MR brain scans + +*Sedation:* Rats were anesthetized with 1.5 % isoflurane in 1:1 O2:N2 during +surgery, placing the animal in the MRI scanner and during the anatomical scan. + +*MR Scanner:* MRI data were acquired using a 9.4 T Bruker AVANCE III small- +animal MRI scanner (20 cm bore) equipped with a BGA12S gradient system. A +112/086 1H volume resonator was used for transmitting and a 1H 20 mm single-loop +coil for signal receiving. All parameters, data acquisition and reconstruction +was controlled by ParaVision 7 software. + +*MR Sequence:* For the anatomical MRI a 2D T2-weighted TurboRARE sequence (echo +time/repetition time = 25/2600 ms, matrix = 256 x 256, 25 slices, +resolution = 0.1 x 0.1 mm in plane, 0.8 mm slice thickness, 4 averages, scan +time = 4 minutes) was used. + +### Whole-brain Light Sheet imaging + +*Sedation:* For ex vivo preparation, rats were deeply anesthetized with 0.6 ml +of ketamine (500 mg / 10 ml) and Rompun (2 %) in a 1:1 mixing ratio. + +*Clearing and staining:* Clearing was performed according to a custom organic +solvent-based ECI clearing protocol. Nuclei were stained using TOPRO1. + +*Light Sheet imaging:* Light Sheet images were acquired using a UltraMicroscope +Blaze by Milteny Biotec with a 1.10 objective and 0.6 zoom, 5 μm light sheet +thickness and 2 μm slice stepping. The software ImspectorPro v7.3.6 was used. +The excitation and emission spectra were 510/20 nm and 540/20 nm for TOPRO1 in +channel 1, and 590/20 nm and 625/30 nm for auto fluorescence in channel 2. Both +channels are 16 bit encoded and sampled on a 2048 x 2048 pixel grid with 9.85 μm +isotropic pixel size. + +## Data organization + +This dataset is organized as Annotated Research Context (ARC), i.e. it follows +the ARC directory structure, naming conventions and metadata scheme. See +https://arc-rdm.org for details. The dataset is structured as shown below. The +Light Sheet data stored as 4D OME-TIFF stack with channels and z-slices in +separate files and the MRI data is stored in a 3D DICOM stack with z-slices in +separate files. The ISA-Tab (https://isa-specs.readthedocs.io) formatted Excel +files and protocols sub-directories contain additional metadata. -## Authors and acknowledgment -Show your appreciation to those who have contributed to the project. +``` +. +├── assays +│  ├── LightSheet +│  │  ├── dataset +│  │  │  ├── A114 +│  | │  │  ├── 12-10-27_THR-A-114_TOPRO1-AF-1x0k6-1tile-2LS-2mue-oDynfoc-100ms_Blaze_C00_xyz-Table Z0000.ome.tif +│  | │  │  ├── 12-10-27_THR-A-114_TOPRO1-AF-1x0k6-1tile-2LS-2mue-oDynfoc-100ms_Blaze_C00_xyz-Table Z0001.ome.tif +| | | | : +│  | │  │  ├── 12-10-27_THR-A-114_TOPRO1-AF-1x0k6-1tile-2LS-2mue-oDynfoc-100ms_Blaze_C01_xyz-Table Z0000.ome.tif +│  | │  │  ├── 12-10-27_THR-A-114_TOPRO1-AF-1x0k6-1tile-2LS-2mue-oDynfoc-100ms_Blaze_C01_xyz-Table Z0001.ome.tif +| | | | : +│  │  │  ├── A115 +│  | │  │  ├── 14-09-41_THR-A-115_TOPRO1-AF-1x0k6-1tile-2LS-2mue-oDynfoc-100ms_Blaze_C00_xyz-Table Z0000.ome.tif +| | | | : +│  | │  │  ├── 14-09-41_THR-A-115_TOPRO1-AF-1x0k6-1tile-2LS-2mue-oDynfoc-100ms_Blaze_C01_xyz-Table Z0000.ome.tif +│  | │  │  : +│  │  │  ├── A116 +│  | │  │  ├── 16-27-32_THR-A-116_TOPRO1-AF-1x0k6-1tile-2LS-2mue-oDynfoc-100ms_Blaze_C00_xyz-Table Z0000.ome.tif +| | | | : +│  | │  │  ├── 16-27-32_THR-A-116_TOPRO1-AF-1x0k6-1tile-2LS-2mue-oDynfoc-100ms_Blaze_C01_xyz-Table Z0000.ome.tif +│  | │  │  : +│  │  │  └── A117 +│  | │  │  ├── 11-37-24_THR-A-117_TOPRO1-AF-1x0k6-1tile-2LS-2mue-oDynfoc-100ms_Blaze_C00_xyz-Table Z0000.ome.tif +| | | | : +│  | │  │  ├── 11-37-24_THR-A-117_TOPRO1-AF-1x0k6-1tile-2LS-2mue-oDynfoc-100ms_Blaze_C01_xyz-Table Z0000.ome.tif +│  | │    : +│  │  ├── isa.assay.xlsx +│  │  └── protocols +│  └── MRI +│  ├── dataset +│  │  ├── A114 +│  │  │  └── dicom +│  │  │  ├── MRIm01.dcm +│  │  │  ├── MRIm02.dcm +│  │  │  : +│  │  ├── A115 +│  │  │  └── dicom +│  │  │  ├── MRIm01.dcm +│  │  │  : +│  │  ├── A116 +│  │  │  └── dicom +│  │  │  ├── MRIm01.dcm +│  │  │  : +│  │  └── A117 +│  │  └── dicom +│  │  ├── MRIm01.dcm +│  │  : +│  ├── isa.assay.xlsx +│  └── protocols +│  ├── A114 +│  ├── A115 +│  ├── A116 +│  └── A117 +├── isa.investigation.xlsx +├── README.md +├── runs +├── studies +│  └── Rat_MRI+LS +│  ├── isa.study.xlsx +│  ├── protocols +│  ├── README.md +│  └── resources +└── workflows +``` -## License -For open source projects, say how it is licensed. +## Changelog -## Project status -If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers. +* 2025-01-31 Public Open Data release