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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.

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. Annotations can also be computer aided using the Smart-pen tool. Draw them, stretch them, remove them. 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 slide 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 here. 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: http://bit.ly/camicroscope
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 here.

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 CONTRIBUTING 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 file structure

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 Caracal repository and the distribution 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/camicroscope to 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

	if (!fs.existsSync('./keys/key') && !fs.existsSync('./keys/key.pub') && GENERATE_KEY_IF_MISSING) {
	try {
	execSync(`${preCommand}'/CN=www.camicroscope.com/O=caMicroscope Local Instance Key./C=US'${postCommand}`);
	} catch (err) {
	console.log({err: err});
	}
	}

	data = x;
	delete data['exp'];
	// sign using the mounted key
	var token = jwt.sign(data, signKey, {
	algorithm: 'RS256',

	/**
	* @todo: unit tests for following methods
	* .aggregate()
	* .delete()
	* .find()
	* .update()
	* .distinct()

	try {
	const prikeyPath = './keys/key';
	if (fs.existsSync(prikeyPath)) {
	PRIKEY = fs.readFileSync(prikeyPath, 'utf8');
	} else {
	if (DISABLE_SEC \|\| ENABLE_SECURITY_AT && Date.parse(ENABLE_SECURITY_AT) > Date.now()) {
	PRIKEY = '';
	console.warn('prikey null since DISABLE_SEC and no prikey provided');
	} else {
	console.error('prikey does not exist');
	}
	}
	} catch (err) {
	console.error(err);
	}

	try {
	const pubkeyPath = './keys/key.pub';
	if (fs.existsSync(pubkeyPath)) {
	var PUBKEY = fs.readFileSync(pubkeyPath, 'utf8');
	} else {
	if (DISABLE_SEC \|\| ENABLE_SECURITY_AT && Date.parse(ENABLE_SECURITY_AT) > Date.now()) {
	PUBKEY = '';
	console.warn('pubkey null since DISABLE_SEC and no pubkey provided');
	} else {
	console.error('pubkey does not exist');
	}
	}
	} catch (err) {
	console.error(err);
	}

camicroscope / caracal Goto Github PK

caracal's Introduction

User Guide

Selecting an Image

Viewing an Image

Using Tools

Toolbar Shortcuts

Hosted Setup

Other Resources

Developer Guide

Fast Local Changes

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