From 499f143f0c2db4d2ea344d542ee7d5ffec4197d2 Mon Sep 17 00:00:00 2001 From: Dylan Fong Date: Wed, 30 Oct 2019 10:20:34 -0400 Subject: [PATCH] add old documentation --- documentation/old_documentation.md | 156 +++++++++++++++++++++++++++++ 1 file changed, 156 insertions(+) create mode 100644 documentation/old_documentation.md diff --git a/documentation/old_documentation.md b/documentation/old_documentation.md new file mode 100644 index 0000000..5f17871 --- /dev/null +++ b/documentation/old_documentation.md @@ -0,0 +1,156 @@ +# 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