Closed-loop targeted optogenetic stimulation of C. elegans populations dataset

Citation Author(s):
Mochi
Liu
Princeton University
Sandeep
Kumar
Princeton University
Anuj
Sharma
Princeton University
Andrew
Leifer
Princeton University
Submitted by:
Andrew Leifer
Last updated:
Tue, 08/17/2021 - 15:02
DOI:
10.21227/t6b0-bc36
License:
0
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Abstract 

Here we present recordings from a new high-throughput instrument to optogenetically manipulate neural activity in moving C. elegans that accompany a forthcoming manuscript, Liu et al,  “Closed-loop targeted optogenetic stimulation of C. elegans populations.”  Specifically, the new instrument enables simultaneous closed-loop light delivery to specified targets in populations of moving Caenorhabditis elegans. The instrument addresses three technical challenges: it delivers targeted illumination to specified regions of the animal's body such as its head or tail; it automatically delivers stimuli triggered upon the animal's behavior; and it achieves high throughput by targeting many animals simultaneously. The instrument was used to optogenetically probe the animal's behavioral response to competing mechanosensory stimuli in the the anterior and posterior soft touch receptor neurons. Details of the instrument can be found in the dissertation,  Mochi Liu, “C. elegans Behaviors and Their Mechanosensory Drivers”, Princeton University, 2020.  Associated analysis code is located in https://github.com/leiferlab/liu-closed-loop-code

Instructions: 

Datasets used in the publication:

1) List of all the dataset used to generate figure 2 and 3:

  • 20210614_RunHeadandTailRailswithDelays_AML470_0-20-40-60-80intensity

  • 20210615_RunHeadandTailRailswithDelays_AML470_0-20-40-60-80intensity

  • 20210616_RunHeadandTailRailswithDelays_AML470_0-20-40-60-80intensity

  • 20210617_RunHeadandTailRailswithDelays_AML470_0-20-40-60-80intensity

2) List of all the dataset used to generate figure S3:

  • 20210618_RunHeadandTailRailswithDelays_AML67_0-20-40-60-80intensity

3) List of all the dataset folders used to generate figure 4 and table 1:

a) AML67 dataset, open loop: 

  • 20210624_RunFullWormRails_Sandeep_AML67_10ulRet_red,

  • 20210614_RunFullWormRails_Sandeep_AML67_10ulRet_red,

  • 20200902_RunFullWormRails_Sandeep_AML67_10ulret.

b) AML67 dataset, closed loop: 

  • 20210624_RunRailsTriggeredByTurning_Sandeep_AML67_10ulRet_red,

  • 20210614_RunRailsTriggeredByTurning_Sandeep_AML67_10ulRet_red,

  • 20200902_RunRailsTriggeredByTurning_Sandeep_AML67_10ulRet.

4) List of all the dataset folders used to generate figure 4:

a) AML470 dataset, open loop: 

  • 20210723_RunFullWormRails_Sandeep_AKS_483.7.e_mec4_Chrimson_10ulRet_red,

  • 20210721_RunFullWormRails_Sandeep_AKS_483.7.e_mec4_Chrimson_10ulRet_red,

  • 20210720_RunFullWormRails_Sandeep_AKS_483.7.e_mec4_Chrimson_10ulRet_red.

b) AML470 dataset, closed loop: 

  • 20210723_RunRailsTriggeredByTurning_Sandeep_AKS_483.7.e_mec4_Chrimson_10ulRet_red,

  • 20210721_RunRailsTriggeredByTurning_Sandeep_AKS_483.7.e_mec4_Chrimson_10ulRet_red, 

  • 20210720_RunRailsTriggeredByTurning_Sandeep_AKS_483.7.e_mec4_Chrimson_10ulRet_red/AML470_20210720_turns_0uW_3s_new3.mat')

Instructions for accessing files: 

 

1) Here are the details of the naming convention used in the filenames of the datasets used to generate figure 2, 3, S3.

Let us use the folder name “20210614_RunHeadandTailRailswithDelays_AML470_0-20-40-60-80intensity” as an example. The different components of the names are:

a) Date: In the above example, this dataset was collected on 20210614 (YYYYMMDD).

b) Experiment type: "RunHeadandTailRailswithDelays" represents the data collected by stimulating head, tail, or both.

c) Name of the strain: The above example shows the dataset collected from "AML470" strain. 

d) Experiment specific information: The tag “0-20-40-60-80intensity” says that 0, 20, 40, 60, and 80uW intensity was used during this dataset.

Moreover, once you go inside each folder, you will see many subfolders with the date and time stamp. For e.g. a subfolder in the above folder is Data20210614_141921_BoxA-PC which basically says the time stamp at which this dataset was recorded (DataYYYYMMDD_HHMMSS) followed by the name of the experimental box (BoxA-PC or BoxB-PC or BoxC-PC or BoxD-PC).

2) Here are the details of the naming convention used in the filenames of the datasets used to generate figure 4 and table 1.

Let us use the folder name “20210624_RunRailsTriggeredByTurning_Sandeep_AML67_10ulRet_red” as an example. The different components of the names are:

a) Date: In the above example, this dataset was collected on 20210624 (YYYYMMDD).

b) Experiment type: "RunRailsTriggeredByTurning" represents the data collected in closed loop protocol whereas "RunFullWormRails" represents the data collected in open loop protocol. Thus, the above example represents a dataset collected using closed loop protocol.

c) Name of the user: In the above example, the user is "Sandeep".

d) Name of the strain: The above example shows the dataset collected from "AML67" strain. Folders containing the datasets collected from AML470 will say "AKS_483.7.e_mec4_Chrimson".

e) ATR information: All the datsets used retinal on the OP50 plates to grow the worms, and hence have the tag "10ulRet".

f) Color of the stim: "red" tag says that in this protocol red stimulus was delivered to the worms.

Moreover, once you go inside each folder, you will see many subfolders with the date and time stamp. For e.g. a subfolder in the above folder is Data20210624_105852 which basically says the time stamp at which this dataset was recorded (DataYYYYMMDD_HHMMSS).

Details of files inside each experimental folder:

The dataset is in the form of the output of the real-time LabVIEW instrument for maximum compression. It still needs to go through post-processing before further analysis.

 

Post-processing can be done by running the /ProcessDateDirectory.m MATLAB script from the code repository.

 

It is organized into date directories, which aggregate all the experiments collected on the same day. 

 

Each experiment is it's own time stamped folder within a date directory, and it contains the following files:

- camera_distortion.png contains camera spatial calibration information in the image metadata

- CameraFrames.mkv is the raw camera images compressed with H.265

- labview_parameters.csv is the settings used by the instrument in the real-time study

- labview_tracks.mat contains the real-time tracking data in a MATLAB readable HDF5 format

- projector_to_camera_distortion.png contains the spatial calibration information that maps projector pixel space into camera pixel space

- tags.txt contains tagged information for the experiment and is used to organize and select experiments for analysis

- timestamps.mat contains timing information saved during the real-time experiments, including closed-loop lag.

- ConvertedProjectorFrames folder contains png compressed stimulus images converted to the camera's frame of reference.

Dataset Files