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02: Getting Started

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jaywarrick edited this page Apr 30, 2015 · 4 revisions

Getting Started

After you starting JEX, you will see the following window: ![] (https://github.com/jaywarrick/JEX-Wiki/blob/master/4JEXwindow1.jpg)

  1. Create a new User Profile

  2. Click on “create a new user profile”

  3. Select where you want to save this new profile (e.g., your "Documents" folder)

  4. Type in a name for it as the file name (e.g. Demo).

  5. Click save.

![] (https://github.com/jaywarrick/JEX-Wiki/blob/master/5JEXnewProfile.jpg)

With the user profile file created, we can now store information regarding what disks or servers you would like to use for storing JEX databases (e.g., any folder on a NAS device, external hardrive, or your PC). There will be a .jex file generated in the folder you select. These locations are remembered by this .jex file so you don't have to constantly relocate them each time you open JEX. These locations are termed JEX "Repositories". This is the highest level of organization of data.

  1. Create a new Repository

  2. After you click save new user profile, it will show the following window:

![] (https://github.com/jaywarrick/JEX-Wiki/blob/master/6JEXnewDatabase1.jpg)

  1. Click on “Add Repository”

  2. Select the folder where you want JEX save all the databases, click on it. (eg. I have created an empty folder called myJEX)

![] (https://github.com/jaywarrick/JEX-Wiki/blob/master/7JEXnewDatabase2.jpg)
  1. Click open.
![] (https://github.com/jaywarrick/JEX-Wiki/blob/master/8JEXnewDatabase3.jpg)

If you want to delete a repository, click on the cross button

  1. Create a new Database

  2. Click on the icon that has a green plus sign. You will see the following window:

![] (https://github.com/jaywarrick/JEX-Wiki/blob/master/9JEXnewDatabase4.jpg)

  1. Type in a name for your new database.

  2. Type in any information for this new database.

  3. Type in a password if need.

  4. Click on YES.

![] (https://github.com/jaywarrick/JEX-Wiki/blob/master/10JEXnewDatabase5.jpg)

Now you have a new Database in your Repository.
  1. Click on the icon on the left and it will lead you into JEX workplace of the current database

You can see 7 tabs in the top center of the window. The general rule of thumb is to proceed through the "tabs" of JEX left to right in order (No. 1 to 7).

You are initially brought into JEX with tab “Datasets” active.

![] (https://github.com/jaywarrick/JEX-Wiki/blob/master/11JEXworkplace.jpg)

  1. Create a new Dataset

  2. Click on “Add Dataset” in the bottom center of the window. The following window will show up:

![] (https://github.com/jaywarrick/JEX-Wiki/blob/master/12JEXnewDataset1.jpg)

  1. Type in a name for this new Dataset

  2. Type in any notes of this new Dataset

A Dataset is a 2D array of Entries and is meant to represent something like a well-plate commonly used for cell culture (e.g., a 96-well plate consisting of 8 rows and 12 columns from which one could collect similar types of imaging data); however, feel free to organize your data as you see fit. Each Entry (or well of the well plate) generally will have the same types of objects (e.g., an N-dimensional image object of the image data obtained from that well and a resulting table of data resulting from it's analysis) but each object is unique to that Entry or well. Given each Entry contains data that is independent of data from adjacent Entries but data Objects within each Entry typically depend on one-another. Thus, multi-threading of data analysis is performed at the level of Entries (i.e., analysis of Entries is processed in parallel using the multiple processing cores of the host computer while operations within each Entry are processed linearly/sequentially).

Long story short, you create a Dataset, which is a 2D array of Entries. Now we can import data into each Entry. You can see your array of entries by going to tab #2. Each Entry is displayed as a box. Click the boxes to select particular Entries you would like to import data into (e.g., all of them or just particular row, column, or individual Entry). You can also use the "Quick Selector" on the left side to select locations in the Dataset array.

In this Demo, we use Array Width 1 and Array Height 1 which means I only one entry

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