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Nikon Confocal Microscope Chi-Li Chiu. Nikon confocal microscope demo Oct 7 (Wed)-Oct 15 (Thr) Instrument Features – Simultaneous 4-Channel + DIC confocal.

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Presentation on theme: "Nikon Confocal Microscope Chi-Li Chiu. Nikon confocal microscope demo Oct 7 (Wed)-Oct 15 (Thr) Instrument Features – Simultaneous 4-Channel + DIC confocal."— Presentation transcript:

1 Nikon Confocal Microscope Chi-Li Chiu

2 Nikon confocal microscope demo Oct 7 (Wed)-Oct 15 (Thr) Instrument Features – Simultaneous 4-Channel + DIC confocal imaging – Lasers: 405nm (DAPI), 440nm (CFP), 488nm (GFP), 515nm (YFP), 560nm (RFP), and 640nm (far red) – Objectives: 10x, 20x, 40x, 60x, and 100x – 32-channel Spectral Imaging – TIRF with Andor EMCCD Software Features: – Integrated software platform for acquisition and analysis – NIS- Elements – 3D/4D modeling – Deconvolution module – High content analysis module

3 Nikon confocal microscope demo Oct 7 (Wed)-Oct 15 (Thr) Experiments: – Fixed or live sample – Use glass-bottom dishes/coverslips, or optical grade plastic – Fast acquisition, 3D z stack, multi-color, higher resolution/sensitivity Location: – Between the main lab and Chun-Peng’s office Book the system: http://teamup.com/ksc9f7fef6db669c7e/

4 CAMM Knowledge Base Naim Matasci 25 Sept 2015

5 What’s a Knowledge Base? “A knowledge base (KB) is a technology used to store complex structured and unstructured information used by a computer system.” [Wikipedia] … so like a website?

6 It’s all about Data Organization Comprehensive Indexed Searchable Cross linked Semantically aware – Understanding of “meaning”

7 Adding Context to Data When you generate data, context resides somewhere else – How was the data generated? Sample origin Operator Protocols Equipment and reagents Analyses – Why was the data generated? Goal of the project Experimental design Other related data Other related knowledge Knowledge is dispersed (different people, different supports [e.g. lab notebook, dropbox, spreadsheets, google docs]) Knowledge is compartmentalized

8 Background “Soft” and technical knowledge not recorded or scattered across systems (Dropbox, google docs, wiki.camm, CAMMLAB, personal equipment, etc.) Instrument QC is manually shared/pulled and not centrally recorded and accessible Better standardization of samples, protocols, experimental designs and methods has potential to be highly beneficial

9 Goals Not “Yet another…” One-stop shop for all things CAMM Keep and integrate with existing resources where it makes sense (see CAMMLAB2KB excel spreadsheet) Integrate with data and sample management, and QC (coming) Significant amount of autogenerated content

10 Implementation Wiki-based XWiki: Application Oriented Wiki – Very strong support for structured data (i.e. can also work as a database) – Storage robustness (PostrgeSQL + flat files) – Separation between content and presentation – Very strong ability to be accessed programmatically (i.e. other programs can read and write to it)

11 Important Usability Features Visual editor Rich visual elements (boxes, sortable tables, hidden text…) Markdown based syntax History & Versioning Inline commenting Tagging Extensions (PDF, PPTX viewers,…) Granular access control

12 1 Landing 1.3 Projects1.4 Groups1.6 Admin Target lab personnel For Equipment, protocols, orders and inventory. Target general For Every “project” can have its own page. Some of the pages’ content is autogenerate d from tags. Target general For PIs can create group pages. Automaticall y cross references projects. Page content up to Pis. Target general For Infrastructur e, tutorials, how-tos, code and data. Target general For Forms, USC links, financial (?) 1.2 Computing & Data 1.1 Lab1.5 Jotter Target general For Open space for ideas, suggestions, projects, etc.. Highly granular access control allow to restrict access to areas, pages, etc or make them publicly accessible Design & Content

13 Thematic areas (spaces) Calendars (pulled from google cals) Announcements Activity feeds (personal and global) Tags

14 Logging in: asteroth.camm.usc.edu

15 USER PREFERENCES

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25 ADDING A PAGE

26 Sandbox

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37 Explain what you changed

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44 ADDING A CHILD PAGE

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51 Child pages are not automatically shown in the parent’s content

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