Ref: ExTemp Review

General comments

• Some minor grammar errors in the paper.pdf, e.g. "In particular, since the fluorescent signal comes from dye-labeled DNA, hence temporal DNA barcodes". To me this doesn't read-well
• The text itself seems a little light and hard to understand. I looked at the cited paper in Nano letters and it is explained much better. I raise this as a point in order to make any potential user more aware of what it is this software package does/works with.
• There are no acknowledgements, I see from your previous work that you are funded by National Science Foundation Grants (though, it is mentioned in the readme.MD).
• I don't find author contributions in the paper (though they are in the readme.MD).
• As you are using MATLAB, can you confirm what packages/toolboxes that a user will need, additionally, it would be useful to highlight which MATLAB versions the software should work on.
• I note you used on a HPC equiment to run your experiments, can you comment on if a 'standard' desktop PC is enough for this, or if HPC access is required to perform analysis in regular time?
• Your readme.MD mentions they can be used for any arbitrary microscopy project that requires data extraction from fluorescence microscopy data - perhaps expanding on this and showing some general usecases would be good to make this software useful for a wider audience?
• Have you tested in Octave, it would be useful to know if FOSS software is capable of running these modules rather than closed platforms.
• Do you provide estimations for expected errors from running your software, is there an alternative form of analysis? When similar experiments were ran prior to 2019, how were their data analysed?

Review guidelines to be met:

• If there are any performance claims of the software, have they been confirmed I cannot easily test this, are you able to provide any automated testing with example data
• The above comment also would address the requirements for: example usage, functionality and automated tests.

If findalllocalizations has toDisplay set and a very high threshold value is given for example, 6, then insertFrame raises an error.

For example, findalllocalizations(<file_name>, 6, 1, 1) raised:

Error using insertShape
Expected POSITION to be finite.

Error in insertShape>checkPosition (line 280)
   validateattributes(position, {'numeric'}, ...

Error in insertShape>validateAndParseInputs (line 237)
checkPosition(position);

Error in insertShape (line 106)
    validateAndParseInputs(I, shape, position, varargin{:});

Error in findalllocalizations (line 50)
                localized_frame = insertShape(cur_frame,'circle', [points(:, 1) ...

There is some problem with R2018a when toDisplayFrames=1 as stated here - #4 (comment)

Matlab version: R2018a

Ref openjournals/joss-reviews#2026
Hi, I'm trying to run the demo but it goes with the following error:

Error using lif2mat (line 35)
The size of the right hand side did not match the size of the indexing on the left hand side.

It appears that target frame_size is larger than framebycell.