lowvisionresearch / revas Goto Github PK

Retinal Video Analysis Suite: a utility for generating reference frames and extracting eye position traces from retinal videos recorded via scanning laser ophthalmoscopes. It also includes a set of tools for classifying eye movements into drifts and (micro)saccades, and extracting detailed information about these eye movements.

Home Page: http://selab.berkeley.edu/

MATLAB 99.44% Makefile 0.45% M 0.12%

computer-vision vision-science

revas's Introduction

ReVAS 0.9.9

Retinal Video Analysis Suite: a utility for generating reference frames and extracting eye position traces from retinal videos recorded via scanning laser ophthalmoscopes. It can generate stabilized retinal videos, create reference frames from raw videos, or combine a bunch of reference frames or videos to create large montages. It also includes a set of tools for filtering and classifying eye movements into drifts and (micro)saccades, and extracting detailed information about these eye movements.

Note that this work is still in progress, and a citable paper will be associated with ReVAS in the near future.

Software requirements (to run from source code): Matlab, Image Processing Toolbox, Statistics and Machine Learning Toolbox, Computer Vision Systems Toolbox, Parallel Computing Toolbox.

Software requirements (to run as a standalone application): (to-be-added)

Documentation is available in the Wiki tab of this repository.

Retinal Video Analysis Suite (ReVAS)
by Sight Enhancement Laboratory at Berkeley.
School of Optometry.
University of California, Berkeley, USA.

Mehmet N. Agaoglu, PhD.
[email protected]

Matthew T. Sit.
[email protected]

Derek Wan.
[email protected]

Susana T. L. Chung, OD, PhD.
[email protected]

Additional contributions by: Jason Chen ([email protected]), Alex Yeo ([email protected]), Josselin Gautier, PhD ([email protected]).

Acknowledgments:
uipickfiles 1.13 by Douglas Schwarz.
cprintf by Yair Altman.

MIT License

Copyright 2018 (c) Mehmet N. Agaoglu ([email protected]) (c) Matthew T. Sit ([email protected])
(c) Derek Wan ([email protected])
(c) Susana T. L. Chung ([email protected])

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

revas's People

Contributors

Stargazers

Watchers

Forkers

leinpk elifesciences-publications jwongpadgett swatibhargava-design cludowici perceptual-and-cognitive-dynamics

revas's Issues

[meeting 6/18/18] Update missing info in the tutorials => Derek

Closing ReVAS does not close children GUIs that are open

We need to keep track of the open children GUIs and close them when ReVAS is closed.

After selecting a group of file to be processed and pressing "done", nothing is displayed into "files box" main ReVAS window

important, recurrent and unsolved

[meeting 6/6/18] make the initial size of the main GUI larger.. it's too small and the text is not legible on a Mac. =>Matt

[meeting 6/18/18] Check if "strip analysis" step is necessary to do re-referencing => Joss

Unifying the function headers with authors and links

Hi,
it would be nice, as the code will be open source, that we use the same header like:

% ===========================================================
%  Function FilterStrips    by Mehmet Agaoglu and Matt Sit
%                Sight Enhancement Laboratory at Berkeley 
%                School of Optometry, University of California, Berkeley
%  Please cite this paper: 
%  doi:
% ===========================================================

sample quality plot after Strip Analysis (Fine Ref) has a wrong horizontal axis scaling

After strip analysis at the Fine Ref stage, peak cross-correlations for each individual strip is plotted. But the horizontal axis is wrong. e.g., For a 1000Hz sampling rate in a 1 second video, the axis should be from 0 to 1 second but it goes from 0 to 1000 seconds.

[meeting 6/18/18] Include an example of ReVAS toolbox usage

intermediate video files cannot be found in standalone app

Occurs when ReVAS is used as a standalone app (on macOS Mojave). When all pre-processing steps are disabled (for a previously analyzed video) and only the strip analysis is selected, the program errors out because it cannot find the reference frame file (*_dwt_nostim_gamscaled_bandfilt_refframe.mat) although it does exist in the folder where the video resides.

I found this page as potential reasons why this might be happening http://matlab.wikia.com/wiki/FAQ#Why_can.27t_my_standalone_compiled_executable_find_my_files.3F

[meeting 6/18/18] make the text on GUI fixed size, OR increase the minimum font size => Matt

A search for the optimal min and max Peak Thresholds after error at CoarseRef estimation

[meeting 6/18/18] making a ref frame from a bunch of videos OR combining refs from videos to make a better ref => Mehmet?

[meeting 6/6/18] use position estimates from make ref stages during strip analysis’s initial search window =>?

[meeting 6/18/18] add the option of skipping some frames during ref frame making stages (e.g., use only every other frame or every nth frame). Important for long videos.

can't run from directory containing strip_analysis

I tried to run the GUI using the demo setup, and this failed with:

findblinkframes cannot come after stripanalysis.
06-Nov-2023 15:34:29: ERROR: Pipeline is invalid for _calib. Moving onto next file.

I do not have a stripanalysis item before findblinkframes, findblinkframes is the first thing in the pipeline. Stepping through the code, it turns out the problem is that the path to ReVAS (or the video i am processing, dunno which) contains the folder retinal_strip_analysis, which somehow triggers this first element to be added. I commented out some code and things are ok now, but this seems kinda crazy?

Starting from strip_analysis, some video get "randomly" skipped and not analyzed for no reason => Joss

On several folders containing each on average 10 videos, there is each time 1-2 video not processed
for no apparent reason.

no warnings for overwrite + same Error as in GUI in matlab command window (usefull for // or GPU modes) + status (video#1/10) => Matt?

Tutorial edition: Missing output .mat units

Hi,
I think it would be informative to add the unit in which are expressed the eyePositionTraces in the tutorial.
Because rereferencing is possible, I am inferring that unit are pixels, however because filtering options (saccades detection parameters) are expressed in visual degree, I am not sure if the eyePositionTraces are minutes of arc. Minutes are close to pixel here: for a 10 deg FoV, there are 488 pixels vs 600 minutes.