{"id":102,"date":"2016-05-28T01:55:46","date_gmt":"2016-05-28T01:55:46","guid":{"rendered":"http:\/\/bioimage.coe.drexel.edu\/LEVER\/wordpress\/?page_id=102"},"modified":"2016-12-21T20:17:25","modified_gmt":"2016-12-21T20:17:25","slug":"identify-tree-mitoses","status":"publish","type":"page","link":"https:\/\/bioimage.coe.drexel.edu\/mp\/lever\/index.php\/identify-tree-mitoses\/","title":{"rendered":"identify tree mitoses"},"content":{"rendered":"

‘Identify Tree Mitoses’ provides a fast way to generate a lineage tree from your image data. It does not automatically fix up the segmentation results – for that you need to use ‘resegment from tree’<\/a>. It can be nice to draw the lineage tree first with identify tree mitoses, then ‘Lock the tree’ and finally run ‘resegment from tree’<\/a>.<\/p>\n

Launching this method is similar to resegment from tree.<\/p>\n

Launch LEVER<\/a>, and either (1) segment and track your dataset or (2) open an already segmented and tracked dataset.<\/p>\n

LEVER will open the image window and the lineage window. Arrange the windows on your desktop so you can see them both (hint \u2013 windows key+left arrow and windows key+right arrow).<\/p>\n

Navigate to the edit tab, and then click ‘Identify tree mitoses’\u00a0<\/span><\/p>\n

Scrolling and page up\/down will increment the movie – It will not autoplay like reseg mode.<\/p>\n

When you see a mitosis, click on one of the cells and drag your cursor over to the sibling cell. LEVER will draw hulls around the two cells.<\/p>\n

<\/a><\/p>\n

Continue through the movie, while recording each mitosis. You can switch where on the tree the next mitosis goes by ctrl+clicking on your desired parent.<\/p>\n

Note that error rates are estimated based on the total number of cells and segmentations on the tree. As you edit the tree this may result in error rates >> 100%…do not worry about this. As you resegment from tree, the error rate will decrease dramatically with every frame resegmented.<\/p>\n

When you’re done, lock the lineage tree so that LEVER knows not to mess with the structure.<\/p>\n

 <\/p>\n","protected":false},"excerpt":{"rendered":"

‘Identify Tree Mitoses’ provides a fast way to generate a lineage tree from your image data. It does not automatically fix up the segmentation results – for that you need to use ‘resegment from tree’. It can be nice to draw the lineage tree first with identify tree mitoses, then ‘Lock the tree’ and finally … Continue reading “identify tree mitoses”<\/span><\/a><\/p>\n","protected":false},"author":4,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/bioimage.coe.drexel.edu\/mp\/lever\/index.php\/wp-json\/wp\/v2\/pages\/102"}],"collection":[{"href":"https:\/\/bioimage.coe.drexel.edu\/mp\/lever\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/bioimage.coe.drexel.edu\/mp\/lever\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/bioimage.coe.drexel.edu\/mp\/lever\/index.php\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/bioimage.coe.drexel.edu\/mp\/lever\/index.php\/wp-json\/wp\/v2\/comments?post=102"}],"version-history":[{"count":14,"href":"https:\/\/bioimage.coe.drexel.edu\/mp\/lever\/index.php\/wp-json\/wp\/v2\/pages\/102\/revisions"}],"predecessor-version":[{"id":270,"href":"https:\/\/bioimage.coe.drexel.edu\/mp\/lever\/index.php\/wp-json\/wp\/v2\/pages\/102\/revisions\/270"}],"wp:attachment":[{"href":"https:\/\/bioimage.coe.drexel.edu\/mp\/lever\/index.php\/wp-json\/wp\/v2\/media?parent=102"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}