scverse / scverse/spatialdata-plot
Reproduce Napari visualizations
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enhancement
- 主要语言
- Python
- 星标
- 86
- 派生
- 21
- 平均合并
- 14 小时 50 分钟
- 30 天内合并 PR
- 3
描述
I would like to generate static images files from NGFF/SpatialData datasets and presets stored in their NGFF Omero metadata, so that one can preview datasets without opening them interactively in Napari.
This combines the idea that SpatialData's data model resembles Napari's, and that datasets can store visualization presets for a reasonable default visualization.
For this, we still need some basic rendering properties:
blending:additive|opaque…
Typically, images contain multiple channel, and their visualization is different depending on the microscopy illumination type. Several fluorescence channels can be visualized in a single image by additive blending. However, currently spatialdata-plot "overwrites" pixels of channels underneath.color:
Napari allows to provide a color name for maximum intensity values and generates a corresponding color map.contrast_limits(Napari) orwindow(Omero):
Typically, the value range of images can differ greatly, and in order to avoid reading all pixels to compute limits, Omero stores absolute limits in the metadata. However, spatialdata-plot currently supports only Matplotlib's relative limitspmin/pmax(asquantiles_for_norm).
贡献指南
从这里开始
- 先读完整个 Issue,再读项目的贡献指南。
- 在 Issue 下留言说明你要接手 —— 这能避免两个人做同样的事。
- Fork 仓库,在一个分支上完成修改。
- 提交 Pull Request,并在描述里引用这个 Issue 编号。
调研方向
首先检查现有的 spatialdata-plot 渲染路径,以及 issue 中描述的 NGFF Omero 元数据。确定当前如何读取可视化预设,然后为加性或不透明混合、Napari 风格的颜色,以及绝对对比度限制或窗口定义验收检查项。静态预览能够在不交互式打开 Napari 的情况下复现所请求的预设属性,即视为完成。
由索引模型根据 Issue 内容生成。
评估
- 技术栈
- python
- 领域
- data-visualization
- Issue 类型
- 功能
- 难度
- 5/5
- 预计耗时
- 一周以上
- 活跃度
- 停滞
- 描述清晰度
- 需要澄清
- 新手友好度
- 30/100