TITLE: FIVTools Overview
AUTHORS: William J Buchser

[DESCRIPTION]
Starting point for using FIVTools for image-based functional tools

[STEPS]
SECTION: Installation
2. Within WashU, the program is accessed from the RIS archive below.  Alternatively, this open-source program can be downloaded from the gitlab repo and run directly.

\\storage1.ris.wustl.edu\wbuchser\Active\dB\Software\FIVE_Tools\
SECTION: Installation
1. FIVTools is software designed for use with image-based screens and tools from Washington University's FIVE@MGI and collaborators.
 

SECTION: Loading Image Folder List
5.  Select the folder where the image FOLDERS are housed.  Do not put the subfolder with the actual TIF images (but the parent to that folder).  Paste the name in the box that says "InCell Images dB".  Once you have used that folder name, it will remain in the dropdown for quick selection.

SECTION: Loading Image Folder List
3. Open the program. (It may ask to install an update which you can).
SECTION: Loading Image Folder List
4. Below, you can choose whether the images come from the InCell or ImageXPress microscopes (select the InCell path), or if they are "Non-Standard" (anything else).
6. Press "Refresh" if you have never loaded this folder before, or just "Load dB" to bring up its saved contents.  Refresh will scan through the files and make a new index of them, it will show the list of PlateIDs in the middle region of the window.
SECTION: Work with PlateID (Scan) List
7. Use the "PlateID Contains" to limit the list of scans in the folder to a smaller subset.
  You can type any part of the PlateID name, and a space acts like an "or" operator.  (See above where we want to find experiments 860 and 870 but not the ones inbetween).

"Today" checkbox: filter by images that were taken within the last 24 hours
"Rafts" checkbox: filter to plates that are raft-based
"Analyses" checkbox: only show plateIDs that also have InCarta analyses
SECTION: Loading Image Folder List
5. Click "Open Any Folder"
  Select an image, then press OK.

SECTION: Loading Image Folder List
6. Tell FIVTools some of the information about these images
  The functionality of this is currently limited, images from InCell or ImageXpress are the primary way to use this software

SECTION: Work with PlateID (Scan) List
8. Selecting a PlateID
  Once a PlateID is selected, its InCarta analyses (if any), will show up on the right most panel.  You can also right click to get a context menu with several options.

SECTION: Work with PlateID (Scan) List
8.1. Copy XDCE Info to Clipboard
Click this to copy information about the scan into the clipboard, it is recommended to paste this into a spreadsheet like Excel or Google Docs
SECTION: Work with PlateID (Scan) List
8.2. Open Folder in Explorer, Delete Scan
Opens the folder with the images in your OS for further exploration of the files or Deletes the folder
SECTION: Work with PlateID (Scan) List
8.3. Reconstruct as 5x
Advanced, will link another protocol here
SECTION: Work with PlateID (Scan) List
8.4. Calibrate and Annotate
Equivalent to double-clicking a PlateID or clicking the "CalCheck" button
<Link CalCheck protocol here>
SECTION: Work with PlateID (Scan) List
8.5. Remainder of the items are specific to other protocols, and will be discussed there
SECTION: Work with PlateID (Scan) List
9. Compare two PlateIDs
  Selecting 2 plate IDs (or more) will make the "Comp" button on the bottom middle show up. Clicking this will compare all of the Acquisition protocol metrics.  This is critical if these PlateIDs are part of the same experiment to ensure that no parameters are changed.  If they are, normalization may be required.