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+# TrackStim
+micro-manager plugin to image moving C.Elegans
+
+
+## What is TrackStim
+TrackStim (tracker and stimulater) is a plugin for open source microscopy software called [micro-manager](https://micro-manager.org/wiki/).
+
+This plugin is specialized to help image moving C.Elegans.
+
+This repository is a reupload of the work done by Taizo Kawano.
+
+## Requirements
+
+This plugin needs the following devices:
+- [ASI MS-4000 motorized stage](http://www.asiimaging.com/products/stages/inverted-stages/ms-2000-xyz-automated-stage/)
+- [Hamamatsu Orca R2 CCD camera](http://hamamatsucameras.com/orca-r2/)
+- [Photometrics Dualview beam splitter camera attachment](http://www.biovis.com/photometrics_multichannel.htm)
+
+This plugin requires the following software:
+- [micro-manager 1.3](https://micro-manager.org/wiki/Micro-Manager_Version_Archive)
+
+This plugin also requires a specific directory structure to work
+- TODO find out how the old directory was structured
+
+## Installation
+1.  Put TrackStim_.jar in an appropriate directory. Usually the micromanager/plugin/ folder.
+2.  Restart micor-manager
+3.  Set up micromanager preset. Read the wiki to learn how. [micro-manager](https://micro-manager.org/wiki/).
+4.  Turn on stage controller, camera controller and microscope.
+5.  Open micro-manager.
+6.  In micro-manager main window, choose the preset with these settings:
+      - 128 gain; 4x binning,
+      - 128 digital gain
+      - 100 msec exposure (can be set differently depending on your needs)
+7.  Click the 'image' button and open a preview window.
+8.  Start TrackStim from the plugin menu of imageJ, not the micro-manager plugin menu. You will see the plugin window as below.
+
+![](https://user-images.githubusercontent.com/2328291/58439881-aef82280-80a4-11e9-8553-e1ac57a23d84.png)
+
+## User interface guide
+
+Ready
+: Start tracking object without saving images.
+
+Go
+: Start tracking and imaging.
+
+Stop
+: Stop tracking and imaging.
+
+exposure
+: If SyncDAC connected, exposure time of the camera could be set by this pull down menu. 0, 10, 50, 100, 200, 500, 1000 msec.
+
+Cycle length
+: If SyncDAC connected, set cycle length of imaging. **required to be 2x exposure**. e.g. if exposure is set as 50 msec, cycle length must longer than 100 msec.
+
+Frame num
+: Number of images taken by camera. "one of" option determine how many of them are saved.
+
+1x etc.
+: Stage accelerating modulus.
+
+Yen
+: The thresholding method to perform binary image conversion and object detection.
+
+one of
+: Determine how many images discard. eg. one of 1 means save all images. one of 2 means half of images are saved and rest are throw away. So, If you set 50 msec exposure at micromanager main pannel (20 frame/sec), half of images are saved and resultant data is 10 frame/sec.
+
+Center of Mass
+: Change tracking method. When unchecked it, the plugin track a bright object close to the center of field of view. If checked it, center of mass of whole left half of view is calculated and track it.
+
+manual track
+: Disable tracking features. You have to track object by joystick. The stage position data is still available.
+
+Full field
+: Use whole field of view instead of left half.Only works when using the **Bright field** option
+
+Bright field
+: Using inverted image to detect object. So you can track dark object, not bright one. When you want to track an animal in bright field, enable this and the **Full field** option, and change the Dual-view set up so that the camera take images not split into to wave length.
+
+Save at
+: Assign directly for saved images here. By default saved images are created in a directory named "Untitled#" in every session.
+
+Change dir
+: Sets the directory to **Save at**
+
+### SyncDAC only options
+Light
+: You need check this if you using SyncDAC to apply optical stimulation.
+Run
+: Apply light without taking images
+
+Pre-stim
+: Length or the period before the initial signal.
+
+Strength
+: Light strength. maximum 63.
+
+Duration
+: Length of light signal.
+
+Cycle length
+: Length of one cycle.
+
+Cycle num
+: number of cycles
+
+ramp
+: You can change the strength of light as liner ramp.
+
+base
+: Strength applied interval
+start
+: Strength at the beginning of the duration.
+end
+: Strength at the end of duration.
+
+![](https://user-images.githubusercontent.com/2328291/58440287-fc758f00-80a6-11e9-8759-5ce368f79bc5.png)
+
+
+### Unimplemented commands
+Just closest
+: not implemented
+
+Use right
+: not implemented
+
+
+## System diagram
+![](https://user-images.githubusercontent.com/2328291/58439366-9afef180-80a1-11e9-8453-059f04b7a7dc.png)
+
+TrackStim manages the Real-time processing part in the above figure by processing images captured by the CCD camera to detect bright object and control the motorized stage to track the object.
+
+The coordinate of the stage is stored in header of tiff image file. After the imaging, other programs, such as DVtracer, must be used for further analysis (Post processing part).
+
+## How it works (general algorithm)
+![](https://user-images.githubusercontent.com/2328291/58439437-0f399500-80a2-11e9-9f46-fb7e86f277f7.png)
+
+Let the initial target object be the object closest to the center of the field of view in the initial image.
+
+Then the next target object for the next image is will be the object closest to the target object from the previous image.
+
+Repeat this process for each pair of (previous, current) images.
+
+if the target is separated from the center of view, the StimTrack commands the motorized stage to re-center the target.
+
+### Warnings
+If there are multiple bright objects and the motion is too fast, the program may make mistakes in target tracking.
+
+In the case that the fluorescence signals are not distributed wider than field of view (eg. a few cells in head) enabling "Centor of mass" option may help to achieve stable tracking (see Detailed explanation of interface).
+
+
+## Notes
+This software is provided "as is" and there is no warranty of any kind and no support at all.
+
+Copyright © 2013 Taizo Kawano