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April 18, 2022 17:39
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Omero utility scripts
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javascript:(function(){ | |
let infotab = document.getElementById('infoTab').children[0].children[2]; | |
let channels = infotab.children[0].children[1].children[0].lastElementChild.textContent.trim().split(', '); | |
let channelsliders = document.getElementById('channel_sliders').children[0]; | |
for(i=0;i<channels.length;i++) { | |
let p = document.createTextNode(channels[i]); | |
let br = document.createElement('br'); | |
channelsliders.children[i].insertBefore(br,channelsliders.children[i].firstChild); | |
channelsliders.children[i].insertBefore(p,channelsliders.children[i].firstChild); | |
} | |
})(); |
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javascript:(function(){ | |
let ic = Object.keys(angular.element(document.getElementsByClassName('channel-group-headers')).scope().model.indexedChannels).length; | |
for(i=0;i<ic/4;i++) { | |
angular.element(document.getElementsByClassName('btn-add-channel-group')).click(); | |
angular.element(document.getElementsByClassName('channel-group-headers')).scope().model.channelGroups[i].name= 'Cycle '+i; | |
angular.element(document.getElementsByClassName('channel-group-headers')).scope().model.channelGroups[i].channels = [4*i,4*i+1,4*i+2,4*i+3]; | |
angular.element(document.getElementsByClassName('channel-group-headers')).scope().model.channels[4*i].color="#0000FF"; | |
angular.element(document.getElementsByClassName('channel-group-headers')).scope().model.channels[4*i+1].color="#00FF00"; | |
angular.element(document.getElementsByClassName('channel-group-headers')).scope().model.channels[4*i+2].color="#FFFFFF"; | |
angular.element(document.getElementsByClassName('channel-group-headers')).scope().model.channels[4*i+3].color="#FF0000"; | |
} | |
angular.element(document.getElementsByClassName('channel-group-headers')).scope().model.channelGroups[ic/4].channels = []; | |
})(); |
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javascript:(function(){ | |
var imgId = parseInt(document.getElementById('info').children[0].children[3].children[0].children[0].textContent.split(': ')[1]); | |
var headers = ['Name', 'X', 'Y', 'RadiusX', 'RadiusY', 'Width', 'Height']; | |
var url = `https://omero.hms.harvard.edu/api/v0/m/images/${imgId}/`; | |
var urlRoi = `https://omero.hms.harvard.edu/api/v0/m/rois/?image=${imgId}`; | |
var imgName; | |
fetch(url) | |
.then(res => res.json()) | |
.then(resJson => | |
imgName = resJson.data.Name | |
) | |
.then(() => fetch(urlRoi) | |
.then(res => res.json()) | |
.then(resJson => | |
resJson.data | |
.map(data => { | |
data.shapes[0].Name = data.Name || 'undefined'; | |
return data.shapes | |
}) | |
.reduce((acc, val) => acc.concat(val), []) | |
.map(shape => headers.map(header => shape[header] || -1)) | |
) | |
.then(rois => rois.map(e => e.join(",")).join("\n")) | |
.then(roisStr => | |
"data:text/csv;charset=utf-8," + | |
headers.join(',') + '\n' + | |
roisStr) | |
.then(fullStr => encodeURI(fullStr)) | |
.then(uri => { | |
let link = document.createElement("a"); | |
link.setAttribute("href", uri); | |
link.setAttribute("download", `${imgName}-${imgId}-rois.csv`); | |
document.body.appendChild(link); | |
link.click(); | |
}) | |
) | |
})(); |
Omero ROI extraction works in Omero.iviewer. The script is only slightly modified to work as a bookmarklet. Original creator is @Yu-AnChen
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The script works best as a bookmarklet. Create a new bookmark on your browser's bookmark bar and set the bookmark's location or url as the script above. Example images: https://www.mv.helsinki.fi/home/mckilkki/omero/