Gengstartedwith& OMERO.searcherLocal&...
Transcript of Gengstartedwith& OMERO.searcherLocal&...
Ge#ng started with OMERO.searcher Local
Client v1.3
To download the latest version: h"p://murphylab.web.cmu.edu/so4ware/searcher/
SLF feature sets • The SLF feature sets are described in many of our previous publica?ons (see References at the end) and h"p://murphylab.cbi.cmu.edu/services/SLF/
• OMERO.searcher contentDBs that are currently publicly available use SLF33 and SLF34
• SLF33 can be used for images of any probe depic?ng a subcellular pa"ern – The image does not have to be segmented into individual cells
• SLF34 requires an addi?onal reference image of the nuclear DNA for the same field
SLF33 • SLF33.1-‐SLF33.91 – Haralick texture features calculated at the resolu?on
of the input image and six different levels of downsampling of that image by 2. At each resolu?on, the features are calculated as described for SLF3.66-‐3.78 (Boland and Murphy, 2001)
• SLF33.92-‐SLF33.96 object features (SLF1.1-‐1.5) (Boland and Murphy, 2001) • SLF33.97-‐SLF33.101 edge features (SLF1.9-‐1.13) (
Boland and Murphy, 2001) • SLF33.102-‐SLF33.106 skeleton features (SLF7.80-‐7.84) (Murphy et al 2002) • SLF33.107 the frac?on of fluorescence not contained in objects (SLF7.79)
(Murphy et al 2002) • SLF33.108-‐SLF33.161 parameter free TAS (pfTAS) features calculated by
the modifica?ons (Coelho et al 2010) of the original TAS features (Hamilton et al 2007). 18 features are calculated from the input image plus 18 each calculated at mean and mean-‐margin.
advanced
SLF34 • SLF34 consists of all of the features of SLF33 plus
• SLF34.162-‐163 DNA features SLF2.21 and SLF2.22 (Boland and Murphy, 2001).
• SLF34.164-‐173 addi?onal DNA overlap features.
advanced
Using OMERO.searcher Local Client
• Need to install python and various packages (see installa?on instruc?ons on web site)
• Runs from “command line” or “terminal” • Query images must be in .png, .bmp or .jpg format
• Cri?cal that you know the pixel resolu?on of the query image(s) (in microns/pixel)
Helper scripts • Scripts available for searches of common databases – Two categories of images: ones on your computer and ones on a web site
– Two feature sets, depending on whether a parallel DNA image is available
• searchHPA and getsearchHPA!• searchHPA2 and getsearchHPA2!• searchCELL and getsearchCELL (only)
Using one or more local images • On command line/terminal, type • searchHPA myfolder/*.png!
– (the result will be in a file called searchHPAoutput.html)
• searchHPA myOTHERfolder/*.png OTHER!– (the result will be in a file called searchHPAoutputOTHER.html so that you can keep results separate)
• Assumes that the images are at the same resolu?on at the HPA images (0.08 microns/pixel)
Using an image on the web • On command line/terminal, type • getsearchHPA http://website.org/image.jpg!– (the result will be in a file called getsearchHPAoutput.html)
Using from python • Each command starts with “python omero.search.py” and is followed by various op?ons and the filename(s)
advanced
Op?ons advanced
Common -‐s/-‐-‐server <servername> Specify server/s where images are located -‐f/-‐-‐featureset <featuresetname> Specify featureset to be used -‐r/-‐-‐resolu?on <value> Specify image scale (as a float) -‐n/-‐-‐numimages <value> Specify maximum number of images to return -‐o/-‐-‐output <path> Specify filename for output HTML file
-‐e/-‐-‐everywhere <which> Use all databases available, follow by "localDBs” for ones you have in same directory, or "globalDBs" all known from murphylab website
-‐h/-‐-‐help Print this help message and exit Rare -‐d/-‐-‐db Return list of available databases and exit -‐a/-‐-‐alpha <value> Specify alpha value (as a float) -‐t/-‐-‐tolerance <value> Specify downsample tolerance (as a float)
EXAMPLE SEARCHES USING HUMAN PROTEIN ATLAS IMAGES
Local Client
• Currently available contentDBs – Human Protein
Atlas – PSLID RandTag – The Cell Library – more coming…
Query: DKC1
7/6/13 2:33 PMOMERO.searcher results
Page 1 of 1file:///Users/murphy/Bob/Software/OMERO.searcher/omero.searcher.client-v1.3_fordownload/HPA_DKC1_ch2.html
Query Image(s)
images/proteinatlas/24_A3_1_green.jpg.ch2.bmp
Content Database ['proteinatlas.org-slf33-v2.pkl']Original Scale 0.08Comparison Scale/s [0.08, 0.16, 0.32, 0.64, 1.28]Feature Set slf33Number to Retrieve 10
Results0.08 0.16 0.32 0.64 1.28
Thumbnail ImageData Thumbnail Image
Data Thumbnail ImageData Thumbnail Image
Data Thumbnail ImageData
Info Info Info Info InfoInfo Info Info Info InfoInfo Info Info Info InfoInfo Info Info Info InfoInfo Info Info Info InfoInfo Info Info Info InfoInfo Info Info Info InfoInfo Info Info Info InfoInfo Info Info Info InfoInfo Info Info Info Info
OMERO.searcher results
Query: DKC1
Query: CANX
Query: CANX + DNA
PDIA3 PDIA3 PDIA3
Query: FHIT + DNA
TTBK2 TTBK2 MCOLN3
ADDITIONAL READING
• A. Shariff, J. Kangas, L.P. Coelho, S. Quinn and R.F. Murphy (2010) Automated Image Analysis for High Content Screening and Analysis. J. Biomolec. Screening 15:726-‐734 (available at h"p://murphylab.web.cmu.edu/publica?ons/174-‐shariff2010.pdf)
• B.H. Cho, I. Cao-‐Berg, J.A. Bakal, and R.F. Murphy (2012) OMERO.searcher: Content-‐based image search for microscope images. Nature Methods 9:633-‐634. (available at h"p://murphylab.web.cmu.edu/publica?ons/186-‐cho2012.pdf)