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Brouwer

Dedeke Brouwer

 

 

Software download address:

Download Mplex 4.20 here

 

 

 

Place licence file in the same directory as you placed main program. It is advisable to allow system to use its own addresses unless you want this to be in a special directory.

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Sample DB files for Legendplex     -----   RAT

                                                         -----   HUMAN

(download these to your desired directory)

 

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Sample data sets:

Rat: - zipped directory of some of our data - download entire directory

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Video Tutorials

Part 1: General overview  - (MP4)

Part 2: Explanation of the Cytokine measurement charts  (MP4)

Part 3:  How does AutoGate work and assay assignment  (MP4)

Part 4:  Reading files and data management   (MP4)

 

Video Tutorials from Modena Conference

Example of 6-color analysis: 6 Color Data

Example of debarcoding CyTOF data: Opening and Debarcoding CyTOF

Example of multiplexed cytokine analysis: Cytokines  

Example of gating high-throughput data and data extraction: High-throughput

 

 

Last update May 12 2016 (Check what has been updated)

Please do not distribute any files. The software and data are provided under confidentiality between PUCL and you. Please respect this.

 

Please download the following files.

I suggest you play the tutorials while playing with the files. This way you can follow.

There are more basic tutorials at our EDUCATION page, Tutorials. They may be helpful.

PlateAnalyzer Programs - there are three files - the main file is platAn.exe, there is an INI file which records your file history (and is only created when you first run the program), and your license file. All three files must be in the same directory.  The INI file records your preferences, you past analysis and protocol lists and the layout of your screen. If you have serious problems with the software, you can delete the INI file and it will reset the software to default. You will only loose the history file - which you can easily recreate. The files are coded for your use only. You may use as many copies as you want for your lab use, on as many computers as you want, but they will all be coded with your name.

 

Download the parameters and plate layout files and I suggest you create a directory to identify them as such.

 

General page for Tutorials

PlateAnalyzer QUICK HELP Document (PDF)

Full Plate Examples

Parameter & Plate Layout

Example drug concentration CSV file (use for plates 58 & 65)

Example PAP file for Plate 58 (simple layout)

Example PAP file for Plate 58 (advanced layout)

Example PAP file for Plate 65 (advanced layout)

Example PAP file for Plate 65 (Very advanced layout) this layout shows how you can create an entire report in a single protocol to produce all 96 graphs.

 

Tutorials

1. Here are the tutorials

2. Here is an example video of a large plate (6 million cells) with only one column with positive cells (CD4 Positive)

Parameter & Plate Layout for Cytof Data

 

Vertical Drug Concs. CSV file

Vertical Drug Concs (reversed!!) checking if this is correct!!

Example complex layout for Sunitinib data set (works for others)

More compelex file as on 11/29 call - Sunitinib data set (ditto)

Sunitinib data file DE-BARCODED (418meg zip)

New Logic Map Protocol for March 8 2-12 with New DRUGBOXES

Some of the Tutorials use older versions so icons may have changed, but functionality remains the same.

1. An Introduction (coming from Youtube)to PlateAnalyzer (3 min) This is a 3.5 minute outline of what Plate Analyzer can do (off our server) This shows the general operating features. It's a good place to start. (44meg)

2. Some general videos on PlateAnalyzer (37 sec) comprehensive data management and analysis tool. This is mostly related to drug screening.

3.  Some nice features - Create a new Parameter  (75 Sec)

4. Save graphics from PlateAnalyzer to Word or PPT (33 Sec)

5. So how fast is PlateAnalyzer? Open it, close it, analyze it! (60 sec)

6. New features March 2012 - tracing the analysis pathway

8. SMILES codes read for drugs see YOUTUBE

9.  New DRUGBOX Controls features YOUTUBE

10. Export CSV data files YOUTUBE

11. Dealing with Empty Wells YOUTUBE

12. 40 PLUS parameter data CyTOF analysis YOUTUBE

13. Autowell finder-extracting single wells from large files YOUTUBE

 

March 2013- Auto Well finder - Accuri, CyAN flow data

There is a new feature in PlateAnalyzer. You can now take native files collected on the Accuri or CyAN via the Hypercyt and separate the files based on time/well number into separate list mode files for each well. The AutoWellfinder has some nice features for cleaning up data, and can read sets of files such as created by Accuri or the single time-based files from CyAn. There is no size limit. Here is the MP4 tutorial (13 megs) to explain how to use this feature or you can go to YouTube.

 

SMILES - addition of link to PUBCHEM and reading CSV files

You can read SMILES codes for drugs with PlateAnalyzer. You must create a CSV file in the exact format as the one HERE. Don't change the number of columns. Just replace the names and add the smiles code. You can create your own CSV sets and load them from the OPTIONS, SMILES dripdowns.

 

 

 

 

Tutorials (mainly for Cytof users)

 

1. Initial Ideas (Sept 26, 2010)

2. Here are the general  tutorials

3. Specific tutorial for Bodenmiller data only (37 meg)

4. Decoding Tutorial is here (4.6 meg)

5. My Video of Checker (2 dec) (5meg)

6. My Video of Starsnstripes (2 dec - low audio sorry!) (7meg)

7. March 8, 2012 - New Drugbox controls

Additional Cytof Tutorials

 

CyTOF only:

Special Program for De-Barcoding (see tutorial) (modified Dec 2, 2011 - you can now leave in the barcoded data (check) or leave it out.

Advanced Very High Content (VHC) Analysis (CyTOF data)

1. Cytof data from Bernd Bodenmiller (43 raw variables inc 7 barcodes with 2.3 Million cells) (actually this analysis video uses all 2.3 million cells not just 10% as I say in the video...OR WATCH THIS ON YOUTUBE ITS FASTER so it's a pretty big data set and still operates interactively in real time) 7.5 min

 

 

 

 

Programs

32 bit:

  • PlatAn.exe   (the latest version of the main program)
  • PlatAn.ini   (can be deleted any time but it remembers what you have done - if you have major problems and the program seems possessed, just deleted this file and start again). The main program installation is in c:/program files (x86)/PUCL/Plate Analyzer (x86 for 64 bit) and c/:program files/PUCL/Plate Analyzer (for 32bit computers). The download is to your /users/name directory (windows 7 does not allow editing files in main program directory) but the program is run from the c:/program files  directory and this is where you MUST place your LIC file.

 

64 bit version PlateAnalyzer:

Here is the 64 bit version. This is an automatic download

1. 64 bit version: Download

 

  • Platan.lic  (your license file which must remain with the exe) This is specific to you and has your name in it. Protect it as if you disctibute this file, others can use your copy of plateanalyzer - but it will always show your name!!

 

Plate Analyzer is a project from the Purdue Univeristy Cytometry Laboratories for both high throughput and high content flow cytometry management and analysis. It has superior capacity to any other program and is order of magnitude faster at achieving data processing & analysis. It can easily handle 10 million or more cells and 384 well plates and 50-100 parameter data!!! For more information please contact Prof. J. Paul Robinson Email: jpr@flowcyt.cyto.purdue.edu