Definiens Tissue Studio portal 11-24-2014d1641

2015-05-20

Definiens Tissue Studio portal 11-24-2014d1641

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