camicroscope/viewer
camicroscope
viewer frontend components
下载次数: 0状态：社区镜像维护者：camicroscope仓库类型：镜像最近更新：5 年前
让 AI 帮你使用轩辕镜像？ · 展开查看说明 · 点击收起说明
如果你使用 DeepSeek、元宝 AI、Copilot、ChatGPT 等 AI 工具，协助配置轩辕镜像、编写 docker pull 命令、修改 Docker Compose 镜像地址、配置镜像加速、排查镜像拉取失败、分析报错日志等问题，请先让 AI 阅读并遵守轩辕镜像的规则文档。
只需在 AI 对话中先发送下面这句话即可：
请先完整阅读并严格遵守以下文档中的全部规则与要求：
https://xuanyuan.cloud/agents.md
在未充分阅读并理解该文档前，不要生成任何命令、配置、修改建议、故障排查方案或技术回答。后续所有输出都必须严格以该文档中的规范为最高优先级执行。查看 agents.md 用法指南与完整示范。国内用户首推 元宝 AI、DeepSeek 的深度思考模式，不推荐豆包 AI；Cursor 等编辑器可在对话 @ 该链接，或加入 User Rules。 若 AI 无法访问外链，可 打开说明文档 复制全文粘贴。文档会随站点更新，复制内容可能过期，建议定期检查。
caMicroscope is a web-based biomedical image and data viewer, with a strong emphasis on cancer pathology WSI (Whole Slide Imaging). This guide has sections for different kinds of use of the platform. The User Guide covers the basics on how to use caMicroscope viewer. nanoBorb covers nanoBorb, the version of caMicroscope designed as a standalone application for individual users without a server. Hosted Setup covers how to set up caMicroscope for multiple users on a server. Developer Guide covers the broad strokes on how to add new functionality to caMicroscope.
!View Slides !Measure Features !Annotate Areas of Interest !Alternate Annotation Method !Automatic Object Detection !Test Classification Models
User Guide
Selecting an Image
Depending on what is providing the image metadata, a different login process may be necessary. For public instances, no log in is necessary, and you can proceed to view slides. Use of other tools, such as annotations may or may not require login in this case. For slim instances, login should be done through a redirect directly. For pathDB instances, login should be done on the login link on the main page. At this point, select a collection, if applicable, and proceed to open or "view" the image of your choice.
Viewing an Image
Once an image is open, you can pan around the image by either clicking and dragging (when no conflicting tool, such as the pen, is open), or by moving the red bounding box in the viewport in the bottom right. Zooming can be accomplished through the scroll wheel, pinch events on a touch screen, by using the zoom slider or its associated buttons, or by clicking on the zoom number and inputting a different number.
Using Tools
The toolbar is in the top-left of the main content window. Use the toolbar buttons to manipulate the slide. To close any toolbar button, click the same button again or a new button.
| Tool | Name | Function |
|---|---|---|
| Annotations | Opens the Annotation panel, where you can select which annotation set to view, name that annotation set, add optional notes about the annotation set, save the annotation set, and reset the panel to its original state. | |
| Layer Manager | Opens the Layers Manager panel, where you can select which layers to view. | |
| Home | Return to the data table so that you can open another slide. | |
| Draw | Draw thin lines, thick lines, or polygons on the image. To maintain the integrity of measurements, avoid drawing shapes that overlap or intersect one another. | |
| Preset Labels | Use a preset annotation type immediately to quickly annotate a silde consistently. | |
| Magnifier | The Magnifier works like a magnifying glass and allows you to see the slide at normal magnification (1.0), low magnification (0.5), or high magnification (2.0). Click a magnification level and place the bounding box on the area of the slide you want to magnify. | |
| Measurement | Drag this tool on the slide to learn the measurement in micrometers. | |
| Share View | Opens a window with a URL to the current presentation state of the slide including the magnification level, layers that are currently open, and your position on the image. | |
| Side by Side Viewer | Shows the Layer Manager panel, the left and right layers, and inset window. For the right and left layer, select which layer you want to view. | |
| Heatmap | For a slide with heatmap data, opens the choices of heatmaps available, as well as ways of displaying the heatmaps. The gradient shows all of the values on the selected spectrum for the field you selected. Contains a heatmap edit pen function. | |
| Labeling | Use this tool to draw a circle or rectangle around a tumor region, measure an area on the slide, download labels, and submit a bug report. The Labeling tool has its own toolbar with tools in the following order from left to right: return to the previous slide, place a square on the slide, place a circle on the slide, measure an area, download labels, and submit a bug report. Click the left arrow at the far right of the toolbar to hide it, then click the right arrow to show it. | |
| Segment | This tool allows you to display, count, and export nuclear segmentations on the image. Clicking this tool opens the following custom toolbar. | |
| Model | Show results from a pre-trained tensorflow compatible model on a ROI of the slide. | |
| Download Slide | Download the slide image to your system | |
| Mark Reviewed | Use to signify the completion of review of a slide. | |
| Bug Report | Report a bug or give feedback. | |
| Slide Capture | Click to take a screenshot of the slide and annotations on it. | |
| Tutorial | Click to view a guided tour of the viewer tools. |
Toolbar Shortcuts
| Tool | Shortcut |
|---|---|
| Annotation | Ctrl + a |
| Magnifier | Ctrl + m |
| Measurement | Ctrl + r |
| Side-by-Side | Ctrl + s |
| Close all tools | ESC |
Hosted Setup
The full distribution repository for hosted caMicroscope is https://github.com/camicroscope/Distro/.
run with docker-compose -f caMicroscope.yml up
this will build all services and run in the foreground.
Use docker-compose -f caMicroscope.yml build to rebuild the services.
Once everything is up, go to <the host this is running on>:4010/ to see the landing page.
Other Resources
- Slack: <[***]>
- Discussion mailing list: https://groups.google.com/g/camicroscope
- Sample Tensorflow Models: https://github.com/camicroscope/tfjs-models
Developer Guide
We are collecting feedback to write this section in more detail. Please add your suggestions https://github.com/camicroscope/caMicroscope/issues/267.
caMicroscope is open source software. Any involvement and contribution with the caMicroscope project is greatly appreciated. Feel free to get directly involved in any of the repositories in the caMicroscope organization. New developers may find the notes in https://github.com/camicroscope/caMicroscope/blob/master/CONTRIBUTING.md helpful to start contributing to caMicroscope.
It is highly recommended to make any changes off of the develop branch of a repository, and, when ready, create a PR to the develop branch of the source repository. Before sending the PR, make sure that there are no linting errors by running npm install and then npm run lint to see the errors and npm run lint-fix to automatically fix the errors in the repository folder.
Source code organization ie the file structure of caMicroscope can be found in https://github.com/camicroscope/caMicroscope/blob/master/docs/file_structure.md
Fast Local Changes
When using the hosted setup, you can have the distribution host the changes from your local. Follow these steps :
- Clone this repository, the https://github.com/camicroscope/Caracal/ and https://github.com/camicroscope/Distro/ in the same parent directory
- Set the build to build your local changes instead of the hosted git versions by editing the ca-back container section of your develop.yml. Replace the build context section with the path to your caracal checkout ("../Caracal"), and add
- ../caMicroscope:/src/camicroscopeto the volumes. - Remove this line from 'Dockerfile' in Caracal repository :
RUN git clone https://github.com/${fork:-camicroscope}/camicroscope.git --branch=${viewer:-master}
- In Distro repository, enter the following commands :
docker-compose -f develop.yml build docker-compose -f develop.yml up
镜像拉取方式
您可以使用以下命令拉取该镜像。请将 <标签> 替换为具体的标签版本。如需查看所有可用标签版本，请访问 标签列表页面。
轩辕镜像加速拉取命令点我查看更多 viewer 镜像标签
docker pull docker.xuanyuan.run/camicroscope/viewer:<标签>
DockerHub 原生拉取命令
docker pull camicroscope/viewer:<标签>
镜像拉取常见问题
功能
错误码
用户好评
来自真实用户的反馈，见证轩辕镜像的优质服务
oldzhang
运维工程师
Linux服务器
5
"Docker访问体验非常流畅，大镜像也能快速完成下载。"