> For the complete documentation index, see [llms.txt](https://docs.scenery.graphics/sciview/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.scenery.graphics/sciview/workshops/hip-2021.md). # HIP 2021 The summer school is being hosted in gather: ## Interactive 3D and virtual reality visualization for scientific images with sciview Tutors: * Kyle Harrington, Max Delbrueck Center for Molecular Medicine, * Deborah Schmidt, Max Delbrueck Center for Molecular Medicine, * Giuseppe Barbieri, Center for Advanced Systems Understanding (CASUS) @ HZDR, * Justin Buerger, Center for Advanced Systems Understanding (CASUS) @ HZDR, Sessions: * 2021-09-28 13:00 – 2021-09-28 17:00 CEST For more details here: ## Pre-workshop instructions If you use Windows or MacOS, then we suggest following the **Getting Fiji** instructions. If you use Linux, then we suggest following the **Running sciview through Python** instructions. ### **Getting Fiji** 1. Follow the [Fiji installation instructions](/sciview/installation/installing-fiji.md), if it is not already installed. 2. Install the sciview update site using [these instructions](/sciview/installation/installing-the-development-sciview-plugin-for-fiji.md) ### **Running sciview through Python** (linux only) 1. Install Miniconda, [instructions here](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) 2. Download 3. Unzip the contents and go to that location in your terminal 4. In your terminal: `conda env create -f sciview-hip.yml` 5. In your terminal: `conda activate sciview-hip` 6. In your terminal: `python launch.py` ### **Getting the data** * scripts used in the workshop can be downloaded [here](https://github.com/ida-mdc/sciview-hip-2021) - if you don't want to use git, you can just click the green **Code** button, and click **Download ZIP** * data for the 3D segmentation demo can be downloaded [here](https://cremi.org/static/data/sample_A_20160501.hdf) from the [CREMI challenge](https://cremi.org). The security certificate on the CREMI site is currently expired. Here is a [temporary link](https://www.dropbox.com/s/nwrcz0cai4f7v4m/sample_A_20160501.hdf?dl=0) to the same file. ### **Developers** * Please [sign up for a Github account](https://github.com/join) if you do not already have one. If you are proficient at git, then this is not necessary * To follow along with the developer session, we strongly recommend [downloading IntelliJ](https://www.jetbrains.com/idea/download/). It will be difficult to provide support for any other development environment during the tutorial session. ### Syllabus * Introductions (Kyle, Deborah, Giuseppe, Justin, and everyone attending) * Getting your sciview and development environment setup * Overview of the sciview project * Making your [first scene](/sciview/basics/first-scene.md) * Working with [volumetric data](/sciview/basics/volumetric-data.md) * Working with [meshes](/sciview/basics/mesh-processing.md) * Creating [sciview scripts](/sciview/scripting/first-scripts.md) * Making your [first sciview demo command](/sciview/development/first-demo-command.md) * [Custom point clouds](/sciview/complex-data/point-clouds.md) * [3D segmentation data](/sciview/complex-data/segmentations.md) --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://docs.scenery.graphics/sciview/workshops/hip-2021.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.