Definiens Tissue Studio portal 11-24-2014d1641

2015-05-20

Definiens Tissue Studio is a digital pathology image analysis software application developed and marketed by Definiens AG
-user interface that facilitates machine learning from example digital histopathology images
- Image processing and data analysis are performed either on a local desktop computer workstation, or on a server grid

connect to remote computer to use Definiens Tissue Studio
-Just remote to 10.212.0.15 (when connected to the intranet); 05-08-2015d1630
-go to all programs-> Definiens Developer XD 64 2.0 (choose cell (or maybe in some cases: tissue))

handwritten notes from Diego on using Definiens
-http://azim58.ngrok.io/files/ws-cnio/DR/2015/05%20May/05-18-2015d1422/Definiens?goto=cnio%2FDR%2F2015%2F05%20May%2F05-18-2015d1422%2FDefiniens%2Fhandwritten%20notes%20from%20Diego's%20instruction%20on%20using%20Definiens%2005-17-2015d1316.pdf

Analysis of immunofluorescence confocal images with Definiens Tissue Studio
-put images in folder on image server
-File, new workspace, name workspace
-right click folder, customized import, choose the root folder for the images, select an image for the master file, ok, accept
-Configure analysis button
-Set channels
--General settings, click "edit image layer mixing" to see which colors correspond to each channel.  Set the stain of the nucleus channel and the spot channel
-General settings: 0.1 for 63x maybe
-To run a previously created ruleset, go to button 4 Develop Rulesets, right click in process tree, load ruleset, (a ruleset Elisa has is "nucleus_detection.dax").  Right click added ruleset and select execute.
-zoom tool
-You can analyze intensity per nucleus or spots per nucleus
-configure analysis button
-add detection, DAPI/Het (add)
-background slider, quick tests for backgroun
-low contrast slider
-aberrant shapes
-size variation
-play button
-library save solution, my network places/Img server (Definiens can only process the images located in the img server)
-right click folder, analyze, http:\\definiens:8184
-choose rule set, ok, start
-can come back later on or next day if there are many slides that need to be processed
-manual editing tool
-one click outside, then lasso nuclei
-dropdown, nucleus, button with four spots
-tool to merge selections and delete lines (merge, end line)
-double click image to save it
-could be good to exclude small spots
-object features
-mean layer: 2
-click a spot to see a mean
-Salinger mode only good for nuclei
-process trees; right click, load ruleset
-need Diego for spot detection

azim58wiki: