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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>OMERO.figure</title>
<script>
window.BASE_URL = "";
// For dev, use this server to load/save figures (needs CORS enabled)
const dev_omeroweb_url = "http://localhost:4080/";
// These are updated by views.py when serving this page...
// Flag for knowing if app is served from OMERO (or standalone)
const APP_SERVED_BY_OMERO = false;
const BASE_OMEROWEB_URL = dev_omeroweb_url;
const EXPORT_ENABLED = false;
const SCRIPT_VERSION = "";
const IS_ADMIN = false;
const WEBINDEX_URL = BASE_OMEROWEB_URL + "webclient/";
const BASE_WEBFIGURE_URL = BASE_OMEROWEB_URL + "figure/";
const WEBGATEWAYINDEX = BASE_OMEROWEB_URL + "webgateway/";
const MAKE_WEBFIGURE_URL = BASE_WEBFIGURE_URL + "make_web_figure/";
const UPLOAD_OMERO_SCRIPT_URL = BASE_WEBFIGURE_URL + "upload_omero_script/";
const ACTIVITIES_JSON_URL = WEBINDEX_URL + "activities_json/";
const API_BASE_URL_V0 = BASE_OMEROWEB_URL + "api/v0/"
const STATIC_DIR = "";
const APP_ROOT_URL = "";
const USER_ID = 0;
const PING_URL = "";
const USER_FULL_NAME = "OME";
// hard-code some units for use with vite...
const LENGTHUNITS = {
ANGSTROM: { symbol: "\u00c5", microns: 0.0001 },
CENTIMETER: { symbol: "cm", microns: 10000.0 },
KILOMETER: { symbol: "km", microns: 1000000000.0 },
METER: { symbol: "m", microns: 1000000.0 },
MICROMETER: { symbol: "\u00b5m", microns: 1 },
MILLIMETER: { symbol: "mm", microns: 1000.0 },
NANOMETER: { symbol: "nm", microns: 0.001 },
};
// ...this line replaced with full list by views.py
const LENGTH_UNITS = LENGTHUNITS;
const IS_PUBLIC_USER = false;
// Images larger than this are 'big' tiled images
const MAX_PLANE_SIZE = 10188864;
const MAX_PROJECTION_BYTES = 1024 * 1024 * 256;
// Max active channels for multi-channel images
const MAX_ACTIVE_CHANNELS = 10;
window.MAX_ACTIVE_CHANNELS = MAX_ACTIVE_CHANNELS;
const LOCAL_STORAGE_RECOVERED_FIGURE = "recoveredFigure" + USER_ID;
// Hack! Since the iviewer openwith.js evaluates in global scope and it
// checks for... if ($ && $.jstree)... without this it errors and causes
// the Info panel to fail! jQuery is imported into other scripts as $
const $ = undefined;
</script>
<!-- Use cdn for vite, but this is served from static by Django -->
<link
rel="stylesheet"
href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.11.0/font/bootstrap-icons.css"
/>
</head>
<body id="body">
<!-- Welcome splash-screen Modal -->
<div
class="modal"
id="welcomeModal"
tabindex="-1"
role="dialog"
aria-hidden="true"
>
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Welcome to OMERO.figure</h5>
<button
type="button"
class="btn-close"
data-bs-dismiss="modal"
aria-label="Close"
></button>
</div>
<div class="modal-body" style="padding: 25px 25px 35px 25px">
<p>To get started...</p>
<div
style="
margin-left: auto;
margin-right: auto;
display: block;
width: 70%;
"
>
<!-- Two buttons - use different elements in different ways -->
<button type="button" class="new_figure btn btn-lg btn-primary">
Create New File
</button>
<button
type="button"
class="open_figure btn btn-lg btn-primary float-end"
>
Open File
</button>
</div>
</div>
</div>
</div>
</div>
<!-- About OMERO.figure Modal -->
<div
class="modal"
id="aboutModal"
tabindex="-1"
role="dialog"
aria-hidden="true"
>
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header" style="padding: 15px; text-align: center">
<h5 class="modal-title">About OMERO.figure</h5>
<button
type="button"
class="btn-close"
data-bs-dismiss="modal"
aria-label="Close"
></button>
</div>
<div
class="modal-body"
style="padding: 25px 25px 35px 25px; text-align: center"
>
<p>
<strong>Version</strong>:
<span id="release_version"></span>
</p>
<p>
For more information, visit the
<a
target="new"
href="https://www.openmicroscopy.org/omero/figure/"
>OMERO.figure Home Page</a
>
</p>
<p>
© 2013-{% now "Y" %} University of Dundee & Open
Microscopy Environment<br />
OMERO is distributed under the terms of the GNU GPL and
OMERO.figure under AGPL.<br />
See:
<a target="new" href="http://www.openmicroscopy.org"
>openmicroscopy.org</a
>
</p>
</div>
<div class="modal-footer" style="margin-top: 0">
<button
type="button"
class="btn btn-default"
data-bs-dismiss="modal"
>
Close
</button>
</div>
</div>
</div>
</div>
<!-- ROI editing modal dialog -->
<div
class="modal"
id="roiModal"
data-backdrop="static"
tabindex="-1"
role="dialog"
aria-hidden="true"
>
<div class="modal-dialog" style="width: 950px; max-width: 950px;">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title" style="float: left; padding-right: 20px">
Edit ROIs
</h5>
<p style="margin: 4px 0 0 0">
Draw & edit ROIs and load ROIs from OMERO
</p>
</div>
<div
id="roi_toolbar"
class="roi_toolbar btn-toolbar"
role="toolbar"
aria-label="..."
></div>
<form class="roiModalForm" role="form">
<div id="roi_zt_buttons" style="margin-left: 25px"></div>
<div class="modal-body row">
<div class="col-8">
<div id="roiViewer" class="roiViewer">
<!-- Show / add ROIs on image -->
<!-- <div id="roi_image" style="position: absolute"> -->
<img class="roi_image" style="position: absolute" />
<!-- </div> -->
<div
id="roi_paper"
class="roi_paper"
style="
position: absolute;
top: 0;
left: 0;
overflow: hidden;
"
>
<!-- svg is added here by Raphael.js -->
</div>
</div>
</div>
<div id="roiModalSidebar" class="col-4" style="padding: 0"></div>
</div>
<div class="modal-footer" style="margin-top: 0">
<button type="button" class="btn btn-default" data-bs-dismiss="modal">Cancel</button>
<button type="submit" class="btn btn-primary">OK</button>
</div>
</form>
</div>
</div>
</div>
<!-- Confirm modal for custom messages -->
<div
class="modal"
id="confirmModal"
data-backdrop="static"
tabindex="-1"
role="dialog"
aria-hidden="true"
>
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Save Changes to Figure?</h5>
</div>
<div class="modal-body" style="padding: 25px 25px 35px 25px">
<p>Your changes will be lost if you don't save them</p>
</div>
<div class="modal-footer" style="margin-top: 0">
<button
type="button"
class="btn btn-default"
data-bs-dismiss="modal"
>
Don't Save
</button>
<button
type="submit"
class="btn btn-primary"
data-bs-dismiss="modal"
>
Save
</button>
</div>
</div>
</div>
</div>
<!-- Paper setup Modal -->
<div
class="modal"
id="paperSetupModal"
tabindex="-1"
role="dialog"
aria-hidden="true"
>
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Paper Setup</h5>
<button
type="button"
class="btn-close"
data-bs-dismiss="modal"
aria-label="Close"
></button>
</div>
<form class="paperSetupForm" role="form">
<div class="modal-body">
<!-- Content added from paper_setup_modal_template -->
</div>
<div class="modal-footer" style="margin-top: 0">
<button
type="button"
class="btn btn-default"
data-bs-dismiss="modal"
>
Cancel
</button>
<button type="submit" class="btn btn-primary">OK</button>
</div>
</form>
</div>
</div>
</div>
<!-- chgrp Modal -->
<div
class="modal"
id="chgrpModal"
tabindex="-1"
role="dialog"
aria-hidden="true"
>
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Move Figure to Group</h5>
<button
type="button"
class="btn-close"
data-bs-dismiss="modal"
aria-label="Close"
></button>
</div>
<form class="chgrpForm" role="form">
<div class="modal-body">
<!-- Content added -->
</div>
<div class="modal-footer" style="margin-top: 0">
<button
type="button"
class="btn btn-default"
data-bs-dismiss="modal"
>
Cancel
</button>
<button type="submit" class="btn btn-primary">OK</button>
</div>
</form>
</div>
</div>
</div>
<!-- dpi modal -->
<div
class="modal"
id="dpiModal"
tabindex="-1"
role="dialog"
aria-hidden="true"
>
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Resample Panels</h5>
<button
type="button"
class="btn-close"
data-bs-dismiss="modal"
aria-label="Close"
></button>
</div>
<form class="dpiModalForm form-horizontal" role="form">
<div class="modal-body">
<p>
Set a resolution range for selected panels. When exported as
<strong>PDF</strong>, panel images outside this dpi range will
be resampled as necessary.
</p>
<div
class="form-group"
style="margin-top: 15px; margin-bottom: 0px"
>
<label class="col-sm-4 control-label">
Minimum (optional)
</label>
<div class="row">
<div class="form-group col-sm-11">
<input
type="number"
class="form-control min_export_dpi"
placeholder="min"
/>
</div>
<div class="form-group col-sm-1">
<label style="margin-top:8px">dpi</label>
</div>
</div>
</div>
<div
class="form-group"
style="margin-top: 15px; margin-bottom: 0px"
>
<label class="col-sm-4 control-label">
Maximum (required)
</label>
<div class="row">
<div class="form-group col-sm-11">
<input
type="number"
class="form-control max_export_dpi"
placeholder="max"
/>
</div>
<div class="form-group col-sm-1">
<label style="margin-top:8px">dpi</label>
</div>
</div>
</div>
</div>
<div class="modal-footer" style="margin-top: 0">
<button
type="button"
class="btn btn-default"
data-bs-dismiss="modal"
>
Cancel
</button>
<button type="submit" class="btn btn-primary">OK</button>
</div>
</form>
</div>
</div>
</div>
<!-- Crop Modal -->
<div
class="modal"
id="cropModal"
tabindex="-1"
role="dialog"
aria-hidden="true"
>
<div class="modal-dialog" style="width: 920px; max-width: 920px;">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Crop to Region</h5>
<button
type="button"
class="btn-close"
data-bs-dismiss="modal"
aria-label="Close"
></button>
</div>
<form class="cropModalForm" role="form">
<div
class="modal-body row"
style="height: 500px; max-height: 500px; padding-bottom: 0"
>
<div class="col-4" style="height: 485px; overflow: auto">
<p>
Click and drag on the image to choose a crop region or pick an
ROI from the list below.
</p>
<h4>ROIs:</h4>
<table class="roiPicker roisFromFigure table table-condensed">
<thead>
<td>
<strong
title="Crop to rectangles on this image in the figure"
>from Figure</strong
>
</td>
<td></td>
<td></td>
</thead>
<tbody>
<!-- ROIs loaded here... -->
</tbody>
</table>
<table
class="roiPicker roisFromClipboard table table-condensed"
>
<thead>
<td>
<strong title="Crop to rectangles copied to clipboard"
>from Clipboard</strong
>
</td>
<td></td>
<td></td>
</thead>
<tbody>
<!-- ROIs loaded here... -->
</tbody>
</table>
<table class="roiPicker roisFromOMERO table table-condensed">
<thead>
<td>
<strong
title="Crop to rectangles saved on this image on the OMERO server"
>from OMERO</strong
>
</td>
<td>Z-index</td>
<td>T-index</td>
</thead>
<tbody>
<!-- ROIs loaded here... -->
</tbody>
</table>
<button
style="float: right"
class="btn btn-sm btn-default loadRoiRects"
>
Load More...
</button>
<!-- Additional message/status -->
<p style="color: #999; margin: 10px" id="cropRoiMessage"></p>
</div>
<div class="col-8">
<div id="cropViewer">
<!-- Show / add ROIs on image -->
<div
id="crop_paper"
style="
position: absolute;
top: 0;
left: 0;
right: 10px;
bottom: 10px;
overflow: hidden;
"
>
<!-- svg is added here by Raphael.js -->
</div>
<img
class="crop_image"
style="position: absolute; top: 0; left: 0"
/>
</div>
</div>
</div>
<div class="modal-footer" style="margin-top: 0">
<button
type="button"
class="btn btn-default"
data-bs-dismiss="modal"
>
Cancel
</button>
<button type="submit" class="btn btn-primary" disabled="disabled">
OK
</button>
</div>
</form>
</div>
</div>
</div>
<!-- SetId Modal - behaviour handled by SetIdModalView -->
<div
class="modal"
id="setIdModal"
tabindex="-1"
role="dialog"
aria-labelledby="setIdLabel"
aria-hidden="true"
>
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title" id="setIdLabel">Edit Image ID</h5>
<button
type="button"
class="btn-close"
data-bs-dismiss="modal"
aria-label="Close"
></button>
</div>
<div class="modal-body">
<p>Choose a new Image ID for the selected panels</p>
<form class="setIdForm row g-3">
<div class="col-auto">
<input
type="text"
class="form-control imgId"
placeholder="Image ID"
/>
</div>
<div class="col-auto">
<button type="submit" class="btn btn-primary mb-3 preview">Preview</button>
</div>
</form>
<div class="previewIdChange"></div>
</div>
<div class="modal-footer" style="margin-top: 0">
<button
type="button"
class="btn btn-default"
data-bs-dismiss="modal"
>
Close
</button>
<button
type="submit"
class="btn btn-primary doSetId"
data-bs-dismiss="modal"
disabled="disabled"
>
Update
</button>
</div>
</div>
</div>
</div>
<!-- Color-picker Modal -->
<div
class="modal"
id="colorpickerModal"
tabindex="-1"
role="dialog"
aria-hidden="true"
>
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Color Picker</h5>
<button
type="button"
class="btn-close"
data-bs-dismiss="modal"
aria-label="Close"
></button>
</div>
<form class="colorpickerForm" role="form">
<div class="modal-body" style="height: 300px">
<input class="color-input" type="color" />
<div>Click to Open color-picker</div>
<div
id="demo_cont"
class="demo demo-auto inl-bl"
data-container="#demo_cont"
data-color="#ff0000"
data-inline="true"
>
</div>
<ul class="list-group oldNewColors">
Selected color
<li class="list-group-item"></li>
<li class="list-group-item" style="border-top-width: 0"></li>
Previous color
<div style="margin-top: 55px">Recent colors</div>
</ul>
<div
id="pickedColors"
class="btn-toolbar pickedColors"
role="toolbar"
>
<!-- picked colors added here by render() -->
</div>
</div>
<div class="modal-footer" style="margin-top: 0">
<button
type="button"
class="btn btn-default"
data-bs-dismiss="modal"
>
Cancel
</button>
<button type="submit" class="btn btn-primary">OK</button>
</div>
</form>
</div>
</div>
</div>
<!-- LUT-picker Modal -->
<div
class="modal"
id="lutpickerModal"
tabindex="-1"
role="dialog"
aria-hidden="true"
>
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Lookup Table Chooser</h5>
<button
type="button"
class="btn-close"
data-bs-dismiss="modal"
aria-label="Close"
></button>
</div>
<div class="modal-body row" style="height: 500px">
<p>Loading Lookup Tables...</p>
</div>
<div class="lutPreview lutBg"> </div>
<div class="modal-footer" style="margin-top: 0">
<button
type="button"
class="btn btn-default"
data-bs-dismiss="modal"
>
Cancel
</button>
<button type="submit" class="btn btn-primary" disabled="disabled">
OK
</button>
</div>
</div>
</div>
</div>
<!-- Add-Images Modal - behaviour handled by AddImagesModalView -->
<div
class="modal"
id="addImagesModal"
tabindex="-1"
role="dialog"
aria-hidden="true"
>
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Add Images</h5>
<button
type="button"
class="btn-close"
data-bs-dismiss="modal"
aria-label="Close"
></button>
</div>
<form class="addImagesForm" role="form">
<div class="modal-body">
<p class="omero_only_element">
Add images to the figure by entering their IDs, separated by
commas.<br />
Hint: You can also select images in the webclient, click the
link in right panel, copy the URL and paste it here:
</p>
<p class="standalone_only_element">
Add OME-Zarr images to the figure by entering their full URL:
</p>
<div
class="form-group"
style="margin-top: 15px; margin-bottom: 0px"
>
<input
type="text"
class="form-control imgIds"
placeholder="Image IDs or URL"
/>
</div>
</div>
<div class="modal-footer">
<button
type="button"
class="btn btn-default"
data-bs-dismiss="modal"
>
Close
</button>
<button
type="submit"
class="btn btn-primary"
data-bs-dismiss="modal"
disabled="disabled"
>
Add Images
</button>
</div>
</form>
</div>
</div>
</div>
<!-- /.modal -->
<!-- Export json Modal -->
<div
class="modal"
id="exportJsonModal"
tabindex="-1"
role="dialog"
aria-hidden="true"
>
<div class="modal-dialog" style="width: 800px">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Export as JSON</h5>
<button
type="button"
class="btn-close"
data-bs-dismiss="modal"
aria-label="Close"
></button>
</div>
<form class="addImagesForm" role="form">
<div class="modal-body">
<p>
The current Figure is entirely defined by the JSON data below.
</p>
<div
class="form-group"
style="margin-top: 15px; margin-bottom: 0px"
>
<textarea class="form-control" rows="15"></textarea>
</div>
</div>
<div class="modal-footer">
<button
type="button"
class="btn btn-default"
data-bs-dismiss="modal"
>
Close
</button>
</div>
</form>
</div>
</div>
</div>
<!-- Import json Modal -->
<div
class="modal"
id="importJsonModal"
tabindex="-1"
role="dialog"
aria-hidden="true"
>
<div class="modal-dialog" style="width: 800px">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Import from JSON</h5>
<button
type="button"
class="btn-close"
data-bs-dismiss="modal"
aria-label="Close"
></button>
</div>
<form class="importJsonForm" role="form">
<div class="modal-body">
<p>Paste the JSON data for the Figure into the text box below.</p>
<div
class="form-group"
style="margin-top: 15px; margin-bottom: 0px"
>
<textarea class="form-control" rows="15"></textarea>
</div>
</div>
<div class="modal-footer" style="margin-top: 0">
<button
type="button"
class="btn btn-default"
data-bs-dismiss="modal"
>
Cancel
</button>
<button type="submit" class="btn btn-primary">OK</button>
</div>
</form>
</div>
</div>
</div>
<!-- Markdown Info Modal -->
<div
class="modal"
id="markdownInfoModal"
tabindex="-1"
role="dialog"
aria-hidden="true"
>
<div class="modal-dialog" style="width: 800px">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Label Formatting</h5>
<button
type="button"
class="btn-close"
data-bs-dismiss="modal"
aria-label="Close"
></button>
</div>
<div class="modal-body" style="max-height: 542px">
<h4>Markdown formatting</h4>
<p>
You can use "Markdown" syntax to add formatting to plain text. For
example, **this text will be bold** and this *word* will be italic.
</p>
<p>
NB: Links are not supported for panel labels.
</p>
<p>
NB: You can escape a certain character to not be interpreted as Markdown by adding \ in front of the
character. Ex: "my_string_" is interpreted as "my<i>string</i>" but "my\_string\_" is now interpreted as "my_string_"
</p>
<table class="table">
<tr>
<td></td>
<th>This text will be formatted to...</th>
<th>...this text</th>
</tr>
<tr>
<th>BOLD</th>
<td>Use 2 stars for **bold**.</td>
<td>Use 2 stars for <strong>bold</strong>.</td>
</tr>
<tr>
<th>ITALIC</th>
<td>Use 1 star for *italic*.</td>
<td>Use 1 star for <i>italic</i>.</td>
</tr>
<tr>
<th>LINKS</th>
<td>Add links with [Link text](http://link_url.com)</td>
<td>Add links with <a href="#">Link text</a></td>
</tr>
<!-- <tr><td>You need to use 2 line breaks between paragraphs</td><td></td></tr> -->
</table>
<h4>Dynamic properties</h4>
<p>
The drop-down menu in the 'Add Labels' form allows you to create
labels based on Image metadata. Labels created with square
brackets indicate dynamic properties. The properties within the
square brackets will be dynamically updated upon changes.
Additional text can be added outside the square brackets and will
not be affected when the labels are displayed.<br />
The following table shows some examples, including the use of
dynamic properties and markdown together.
</p>
<table class="table">
<tr>
<td></td>
<th>This text will be formatted to...</th>
<th>...this text</th>
</tr>
<tr></tr>
<tr>
<th>X and Y in pixels</th>
<td>X:[x.pixel] - Y:[y.pixel]</td>
<td>X:52 - Y:89</td>
</tr>
<tr>
<th>X and Y in units</th>
<td>X:[x.unit] - Y:[y.unit]</td>
<td>X:0.43 µm - Y:0.23 µm</td>
</tr>
<tr>
<th>Width</th>
<td>Width: [width.pixel]</td>
<td>Width: 400</td>
</tr>
<tr>
<th>Height (with markdown formatting)</th>
<td>*Height*: **[height.pixel]**</td>
<td><i>Height</i>: <strong>300</strong></td>
</tr>
<tr>
<th>Width with decimal precision of 3</th>
<td>Width: [width.unit; precision=3]</td>
<td>Width: 4.450 µm</td>
</tr>
<tr>
<th>Time relative to the 3rd frame</th>
<td>Time: [time.milliseconds; offset=3]</td>
<td>Time: -58 ms</td>
</tr>
<tr>
<th>
Time with decimal precision 2, <br />relative to the 3rd frame
</th>
<td>Time: [time.seconds; precision=2; offset=3]</td>
<td>Time: -0.06 s</td>
</tr>
<tr>
<th>Z index with units <br/> (first plane is Z: 0.00 µm), <br/>offset by 3 times the Z pixel size</th>
<td>Z: [z.unit; offset=3]</td>
<td>Z: -3.00 µm </td>
</tr>
<tr>
<th>Z index (first plane is Z: 1) <br/>offset by 3</th>
<td>Z: [z.pixel; offset=3]</td>
<td>Z: -2 </td>
</tr>
<tr>
<th>Image ID</th>
<td>Image ID: [image.id]</td>
<td>Image ID: 23556</td>
</tr>
<tr>
<th>Dataset ID</th>
<td>Dataset ID: [dataset.id]</td>
<td>Dataset ID: 1654</td>
</tr>
<tr>
<th>Well, Field</th>
<td>Well: [well.label], Field#[field.index]</td>
<td>Well: B2, Field#3</td>
</tr>
<tr>
<th>Run</th>
<td>[run.name]</td>
<td>Run_3_ExpB</td>
</tr>
<tr>
<th>Plate</th>
<td>[plate.name]</td>
<td>Plate_C2</td>
</tr>
<tr>
<th>Screen</th>
<td>[screen.name]</td>
<td>CRISPR_KO_Screen1</td>