When I try to preprocess videos bigger than my JAVA heap memory (34Gb, max allowed) I get the error below and I was wondering how can I analyse videos with size bigger than that.
Thank you very much in advance for your help

pre-allocating single ones matrix: 800 1280 38801
@@@@@@@
Error using ones
Requested 800x1280x38801 (148.0GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.
Error in loadMovieList (line 472)
outputMovie = ones(preallocSize,imgClass);
Error in ciatah/modelPreprocessMovieFunction (line 729)
thisMovie = loadMovieList(movieList,'convertToDouble',0,'frameList',thisFrameList,'inputDatasetName',options.datasetName,'treatMoviesAsContinuous',options.turboreg.treatMoviesAsContinuousSwitch,'loadSpecificImgClass','single');
Error in ciatah/modelPreprocessMovie (line 37)
obj.modelPreprocessMovieFunction('folderListPath',folderListInfo,'fileFilterRegexp',options.fileFilterRegexp,'datasetName',options.datasetName,'frameList',[]);
Error in ciatah/runPipeline (line 202)
obj.(thisFxn{1});
Error in ciatah/display (line 6)
obj.runPipeline;
@@@@@@@
pre-allocating movies to display...
+++++++
no movie!

MIJ 1.3.9: Matlab to ImageJ Interface

More Info: http://bigwww.epfl.ch/sage/soft/mij/
Help: MIJ.help
JVM> 1.3.9
JVM> Version: 1.8.0_181
JVM> Total amount of memory: 387584 Kb
JVM> Amount of free memory: 244514 Kb
ImageJ> Version:1.53k
ImageJ> Memory:141MB of 29964MB (<1%)
ImageJ> Directory plugins: Not specified
ImageJ> Directory macros: Not specified
ImageJ> Directory luts: C:\Users\realtime\Documents\MATLAB\luts
ImageJ> Directory image: Not specified
ImageJ> Directory imagej: C:\Users\realtime\Documents\MATLAB
ImageJ> Directory startup: C:\Users\realtime\Documents\MATLAB
ImageJ> Directory home: C:\Users\realtime\

Status> ImageJ is running.

Warning: The DrawMode property will be removed in a future release. Use the
SortMethod property instead.

In ciapkg.overloaded.msgbox (line 280)
In ciatah/modelPreprocessMovieFunction>playOutputMovies (line 2432)
In ciatah/modelPreprocessMovieFunction (line 1090)
In ciatah/modelPreprocessMovie (line 37)
In ciatah/runPipeline (line 202)
In ciatah/display (line 6)
+++++++
no movie!
ImageJ instance ended cleanly

Hi there, I've been trying to get ciatah working on my ubuntu 20.04 machine. After some tinkering I've got videos loaded and can even take a folder with a bunch of UCLA miniscope avi files through the viewMovieRegistrationTest step.

However, when I try and run that same folder with the same regex strings through modelPreprocessMovie I get a blank image for selecting the ROI for motion correction. If I drag and double click anyway, i get an indexing error (see below).

I'm not 100% sure of the workflow here, if it would be better for me to try and downsample and convert to h5 first (running modelDownsampleRawMovies throws no errors but produces no output). Any help would be greatly appreciated!

@@@@@@@
Index in position 1 is invalid. Array indices must be positive integers or logical values.

Error in ciatah/modelPreprocessMovieFunction>localfxn_turboregCropSelection (line 2563)
thisFrameCropped = thisFrame(pts(2):pts(4), pts(1):pts(3));

Error in ciatah/modelPreprocessMovieFunction (line 637)
[turboRegCoords] = localfxn_turboregCropSelection(options,folderList);

Error in ciatah/modelPreprocessMovie (line 42)
obj.modelPreprocessMovieFunction('folderListPath',folderListInfo,'fileFilterRegexp',options.fileFilterRegexp,'datasetName',options.datasetName,'frameList',[]);

Error in ciatah/runPipeline (line 209)
obj.(thisFxn{1});

Error in ciatah/display (line 6)
obj.runPipeline;
@@@@@@@
Warning: User likely did not give calciumImagingAnalysis a proper raw input file regular expression or incorrect HDF5 input dataset
name!

In ciatah/modelPreprocessMovieFunction (line 642)
In ciatah/modelPreprocessMovie (line 42)
In ciatah/runPipeline (line 209)
In ciatah/display (line 6)

Hi, I'm trying to run the viewMovieRegistrationTest Pipeline with the example images provided, but I am not able to proceed with the pipeline; I don't see the images I want to see at the end of the pipeline. How can I go around this? I get the following errors:

_movieList = 0×0 empty cell array

Index exceeds the number of array elements (0).

Error in ciatah/viewMovieRegistrationTest>subfxnCropSelection (line 472)
inputFilePath = movieList{movieNo};

Error in ciatah/viewMovieRegistrationTest (line 114)
[registrationCoords] = subfxnCropSelection(toptions,folderList);

Error in ciatah/runPipeline (line 209)
obj.(thisFxn{1});

Error in ciatah/display (line 6)
obj.runPipeline;_

Hi,
My name is Anto and I am relatively new to the use of Ciatah. First of all thank you, it's very very useful!
I had a doubt concerning modelPreprocessMovie and in particular Registration_normalization and Movie_normalization as from the preprocessing options. Filtering and any parameters set in Registration_Noralization are only used to motion correct and not actually applied on the output movie, right? On the other hand, Movie_normalization parameters are used to filter the video and these filtering is actually kept in the output, correct?
Thanks a lot for the clarification!
Best,
Anto

Hello Biafra,

First of all, I would like to thank you for the fantastic job in the Algorithms-based Neuroscience Analysis, it helps me a lot while studying calcium imaging analysis. Although I know nothing about codes, algorithms, Matlab, etc. before Jan. 2021, still I believe I could accomplish more results meaningfully following your amazing Matlab protocols, as its name CIAtah.

However, lately, I got some confusing outputs as below every time when I run obj2 relative commands. Frankly, it has been checked whether it procedurally or manually inappropriate compared with Quick start (command-line) and CIAtah main GUI notes. Sadly, I didnt
find any reasons for them. would you please help me to handle all these errors?

Sincerely appreciate your time!
Benson Kin

@@@@@@@
Dot indexing is not supported for variables of this type.
Error in calciumImagingAnalysis/viewMovie/getProperFrameList (line 738)
nMovieFrames = sum(movieDims.z);
Error in calciumImagingAnalysis/viewMovie (line 287)
[frameListTmp] = getProperFrameList('primary');
Error in calciumImagingAnalysis/runPipeline (line 202)
obj.(thisFxn{1});
Error in calciumImagingAnalysis/display (line 817)
obj.runPipeline;
@@@@@@@

Hey Biafra,

After running cnmf-e or PCA/ICA, I get the same error:

Here is an example of how I get there, perhaps there is a mistake along the way?

(Here I'm still using 'crop' because I chose not to manually modify the movie.)

Then the following Finder window opens up. I'm not sure which file to open here. I tried opening a few different ones, but all led to the same error.

Omid

Hi Biafra,

I am a new user of your analysis pipeline for calcium imaging. First, a big thank you developing this great tool.

We are currently using the pipeline to analyse calcium imaging data acquired with UCLA miniscopes. The data acquisition system saves the miniscope videos in separate files, each with 1000 frames. The videos we want to analyse correspond to a 20min session during wich calcium signals were acquired at 30fps. The initial videos were saved with GREY compression and we had to convert them to .TIF in order to run them through the pipeline.

We successfully managed to run modelPreprocessMovie with a downsampling factor of 4 and got the expected output. Our issue came when running modelExtractSignalsFromMovie with CNMF-E. Apparently out of 37 videos, each with 1000 frames the pipeline only uploaded 1000 frames, leading to the error copied below.

information at the beginning of modelExtractSignalsFromMovie
The data has 608 X 608 pixels X 1000 frames.
Loading all data (double precision) requires 2.754 GB RAM

error message during modelExtractSignalsFromMovie
@@@@@@@
Error using calciumImagingAnalysis/modelExtractSignalsFromMovie/saveRunTimes (line 587)
Unable to perform assignment because the size of the left side is 1-by-1 and the size of the right side is 1-by-37.
Error in calciumImagingAnalysis/modelExtractSignalsFromMovie (line 365)
saveRunTimes('cnmfe');
Error in calciumImagingAnalysis/runPipeline (line 202)
obj.(thisFxn{1});
Error in calciumImagingAnalysis/display (line 817)
obj.runPipeline;
@@@@@@@

Any idea why the pipeline might be skipping the upload of the rest of the data?

All the best,
Miguel

Hi,
When testing the signal extraction on concat_recording_20140401_180333.h5, it is reported that

Could you please help me with it?

Hi,

Is it possible that modelDownSampleRawMovies method can support the avi file? We got the avi video from UCLA miniscope directly but it is too big to be processed in ciatah (30 min video with 4 gb size). I'm considering to downsample these videos but found only TIFF/H5/ISXD are supported.
Do you have any ideas that avi file can be downsampled in ciatah or I can use other software to downsample them?

PS: I tried ffmpeg to downscale or crop the raw video but found the output files lost much quality than I expected. So I'm worried about the following cell extraction effect.

Thank you!
Hemin

Hi Biafra,

We are wondering what exactly are we getting in the traces from the PCA-ICA analysis?
Looking at the traces stored in the PCA-ICA output.mat file we noticed some have negative values. So we are wondering whether these are raw traces or dff?

Thank you!
Natalia

Hi Biafra,

I'm running CIAtah 4.0 on MATLAB R2020b, on a mac.
So far, the speed of the functions and UI are a huge improvement from the previous version! Things run a lot more smoothly.
In the preprocessing step, after the videos are cropped for motion correction, I get the following error:

Omid

Hey Biafra! Since pulling the newest updates in the master, I am running into a new error code after running cnmf-e. Everything seems to be fine until the very end, when I get this error:

... Which leads to this error:

Do you know what could be causing this? I have attached the full command window output.
Omid
Untitled 2.pdf

Hello @bahanonu ! First off, thank you for creating the calciumImagingAnalysis MATLAB package. We are using your software to process some miniscope calcium imaging data. We are trying to interpret some of the output of the registration step (turboreg) and have a few questions. Thank you for the help!

• Can you please explain what the different indices of the ResultsOutOriginal variable (output from the turboreg registration step) correspond to?
• We noticed registration output (e.g., ResultsOutOriginal{1}{1}) has N+1 elements for N video frames. From the log file, it looks like the reference frame may be included. If so, which index is it?
• Are the translation values given for each iteration in ResultsOutOriginal the absolute translation applied to the frame or is it relative to the previous iteration (i.e., to get the total translation, we would have to sum all of the translations across iterations)?

Hi Biafra,
When trying to use NormCorre from the modelPreprocessMovie function in the gui, I run in the error below.
I guess it must be related to me not having run getNoRMCorreParams, but I am not sure..

Thanks again for your help,
Anto

`Getting NoRMCorre params...
@@@@@@@
Unable to resolve the name 'normcorre.NoRMCorreSetParms'.

Error in ciapkg.motion_correction.getNoRMCorreParams (line 75)
optsNC = normcorre.NoRMCorreSetParms(...

Error in ciapkg.motion_correction.turboregMovie/turboregMovieParallel (line 602)
optsNoRMCorre = ciapkg.motion_correction.getNoRMCorreParams(size(inputMovieCropped),'guiDisplay',0);

Error in ciapkg.motion_correction.turboregMovie (line 377)
turboregMovieParallel();

Error in ciapkg.api.turboregMovie (line 10)
[inputMovie, ResultsOutOriginal] = ciapkg.motion_correction.turboregMovie(inputMovie,'passArgs', varargin);

Error in ciatah/modelPreprocessMovieFunction/subfxn_turboregInputMovie (line 2019)
[thisMovie(:,:,movieSubset), ResultsOutOriginal{iterationNo}{thisSet}] = turboregMovie(thisMovie(:,:,movieSubset),'options',ioptions);

Error in ciatah/modelPreprocessMovieFunction (line 906)
subfxn_turboregInputMovie();

Error in ciatah/modelPreprocessMovie (line 42)
obj.modelPreprocessMovieFunction('folderListPath',folderListInfo,'fileFilterRegexp',options.fileFilterRegexp,'datasetName',options.datasetName,'frameList',[]);

Error in ciatah/runPipeline (line 209)
obj.(thisFxn{1});

Error in ciatah/display (line 6)
obj.runPipeline;
@@@@@@@
@@@@@@@
Unable to resolve the name 'normcorre.normcorre_batch'.

Error in ciapkg.motion_correction.turboregMovie/turboregMovieParallel (line 610)
[~,ResultsOut,template2] = normcorre.normcorre_batch(...

Error in ciapkg.motion_correction.turboregMovie (line 377)
turboregMovieParallel();

Error in ciapkg.api.turboregMovie (line 10)
[inputMovie, ResultsOutOriginal] = ciapkg.motion_correction.turboregMovie(inputMovie,'passArgs', varargin);

Error in ciatah/modelPreprocessMovieFunction/subfxn_turboregInputMovie (line 2019)
[thisMovie(:,:,movieSubset), ResultsOutOriginal{iterationNo}{thisSet}] = turboregMovie(thisMovie(:,:,movieSubset),'options',ioptions);

Error in ciatah/modelPreprocessMovieFunction (line 906)
subfxn_turboregInputMovie();

Error in ciatah/modelPreprocessMovie (line 42)
obj.modelPreprocessMovieFunction('folderListPath',folderListInfo,'fileFilterRegexp',options.fileFilterRegexp,'datasetName',options.datasetName,'frameList',[]);

Error in ciatah/runPipeline (line 209)
obj.(thisFxn{1});

Error in ciatah/display (line 6)`

Hi, I keep getting this error during cross registration

folderGlobalIdx: 2  3
@@@@@@@
Unable to perform assignment because the size of the left side is 2855-by-1 and the size of the right side
is 2855-by-2.

Error in ciatah/viewMatchObjBtwnSessions (line 213)
				globalIDs(:,addNo) = globalIDsTmp(:,folderGlobalIdx);

Error in ciatah/computeMatchObjBtwnTrials (line 237)
				obj.viewMatchObjBtwnSessions('runGui',0);

Error in ciatah/runPipeline (line 209)
				obj.(thisFxn{1});

Error in ciatah/display (line 6)
	obj.runPipeline;
@@@@@@@

I tried making it so it just accepted the first folderGlobalIdx but that gave me a bunch of other errors, so I figured I would consult the expert :)

Any help is appreciated. Matlab R2022b, CIAtah v4.5.9. All toolboxes installed. Full traceback:
`1

!!!!!!!!!!!!!!!!!!!!!
Running: obj.modelExtractSignalsFromMovie

options =

struct with fields:

 signalExtractionRootPath: 'C:\Users\rellis01\Documents\MATLAB\ciatah-master\_external_programs'
            saveNwbOutput: 0
            nwbSaveFolder: 'nwbFiles'
           settingsFolder: 'C:\Users\rellis01\Documents\MATLAB\ciatah-master\+ciapkg\+settings'
settingsPrivateSaveFolder: 'C:\Users\rellis01\Documents\MATLAB\ciatah-master\private\settings\signal_extraction'
               nwbYmlPath: 'C:\Users\rellis01\Documents\MATLAB\ciatah-master\_external_programs\nwbpkg\+nwbpkg\ExampleMetadata.yml'

Did not find: extractor.m
Adding folders: C:\Users\rellis01\Documents\MATLAB\ciatah-master_external_programs\extract\EXTRACT\main_functions;C:\Users\rellis01\Documents\MATLAB\ciatah-master_external_programs\extract\EXTRACT\main_functions\debug_utils;C:\Users\rellis01\Documents\MATLAB\ciatah-master_external_programs\extract\EXTRACT\main_functions\debug_utils\brewermap;C:\Users\rellis01\Documents\MATLAB\ciatah-master_external_programs\extract\EXTRACT\main_functions\helper_functions;C:\Users\rellis01\Documents\MATLAB\ciatah-master_external_programs\extract\EXTRACT\main_functions\solvers;
Found: extractor.m
Warning: The DrawMode property will be removed in a future release. Use the SortMethod property instead.

In inputdlg (line 265)
In ciatah/modelExtractSignalsFromMovie (line 121)
In ciatah/runPipeline (line 209)
In ciatah/display (line 6)
Warning: The DrawMode property will be removed in a future release. Use the SortMethod property instead.
In inputdlgcol (line 316)
In ciatah/modelExtractSignalsFromMovie/getAlgorithmOptions (line 1000)
In ciatah/modelExtractSignalsFromMovie (line 167)
In ciatah/runPipeline (line 209)
In ciatah/display (line 6)
=====================
Subject: m000

Getting movie info for 1\1: C:\Users\rellis01\projects\juanita_calcium_analysis_feb2023\5minTL.2023-02-14-15-56-28\dfof_ciatah_video_2_5minTL.2023-02-14-15-56-28.h5
Warning: HDF5 dataset name not found in hinfo.Datasets.Name. Trying another method to load HDF5 dataset.

In ciapkg.io.loadMovieList/getHdf5Info (line 1081)
In ciapkg.io.loadMovieList (line 373)
In ciapkg.api.loadMovieList (line 9)
In ciatah/modelExtractSignalsFromMovie/subfxnSignalSizeSpacing (line 2044)
In ciatah/modelExtractSignalsFromMovie (line 202)
In ciatah/runPipeline (line 209)
In ciatah/display (line 6)
Warning: Could not find /1 in C:\Users\rellis01\projects\juanita_calcium_analysis_feb2023\5minTL.2023-02-14-15-56-28\dfof_ciatah_video_2_5minTL.2023-02-14-15-56-28.h5.
In ciapkg.io.loadMovieList/getHdf5Info (line 1096)
In ciapkg.io.loadMovieList (line 373)
In ciapkg.api.loadMovieList (line 9)
In ciatah/modelExtractSignalsFromMovie/subfxnSignalSizeSpacing (line 2044)
In ciatah/modelExtractSignalsFromMovie (line 202)
In ciatah/runPipeline (line 209)
In ciatah/display (line 6)
Warning: HDF5 hinfo.GroupHierarchy.Groups.Datasets contains no dataset .
In ciapkg.io.loadMovieList/getHdf5Info (line 1111)
In ciapkg.io.loadMovieList (line 373)
In ciapkg.api.loadMovieList (line 9)
In ciatah/modelExtractSignalsFromMovie/subfxnSignalSizeSpacing (line 2044)
In ciatah/modelExtractSignalsFromMovie (line 202)
In ciatah/runPipeline (line 209)
In ciatah/display (line 6)
@@@@@@@
Unrecognized field name "GroupHierarchy".

Error in ciapkg.io.loadMovieList/getHdf5Info (line 1115)
nGroups = length(hinfo.GroupHierarchy.Groups);

Error in ciapkg.io.loadMovieList (line 373)
[hReadInfo, thisDatasetName, datasetDims] = getHdf5Info();

Error in ciapkg.api.loadMovieList (line 9)
[outputMovie, movieDims, nPixels, nFrames] = ciapkg.io.loadMovieList(movieList, 'passArgs', varargin);

Error in ciatah/modelExtractSignalsFromMovie/subfxnSignalSizeSpacing (line 2044)
DFOFList.(thisSubjectStr) = loadMovieList(movieList,'convertToDouble',0,'frameList',[1:500],'inputDatasetName',obj.inputDatasetName,'treatMoviesAsContinuous',1);

Error in ciatah/modelExtractSignalsFromMovie (line 202)
[gridWidth gridSpacing] = subfxnSignalSizeSpacing();

Error in ciatah/runPipeline (line 209)
obj.(thisFxn{1});

Error in ciatah/display (line 6)
obj.runPipeline;
@@@@@@@

Subject: m000
@@@@@@@
Unrecognized function or variable 'DFOFList'.

Error in ciatah/modelExtractSignalsFromMovie/subfxnSignalSizeSpacing (line 2066)
DFOF = DFOFList.(thisSubjectStr);

Error in ciatah/modelExtractSignalsFromMovie (line 202)
[gridWidth gridSpacing] = subfxnSignalSizeSpacing();

Error in ciatah/runPipeline (line 209)
obj.(thisFxn{1});

Error in ciatah/display (line 6)
obj.runPipeline;
@@@@@@@
@@@@@@@
Output argument "gridWidth" (and possibly others) not assigned a value in the execution with "ciatah/modelExtractSignalsFromMovie/subfxnSignalSizeSpacing" function.

Error in ciatah/modelExtractSignalsFromMovie (line 202)
[gridWidth gridSpacing] = subfxnSignalSizeSpacing();

Error in ciatah/runPipeline (line 209)
obj.(thisFxn{1});

Error in ciatah/display (line 6)
obj.runPipeline;
@@@@@@@
Removing unneeded directory from "to add" path list: extractor.m.
Removing unneeded directory from "to add" path list: patchwarp.m.
Adding to JAVA path: C:\Users\rellis01\Documents\MATLAB\ciatah-master_external_programs\bfmatlab_readers\SlideBook6Reader.jar
Folders still need to be removed.
Removing unneeded directory from path: extractor.m.
Removing unneeded directory from path: patchwarp.m.
ImageJ already loaded!
Skipping loading of Miji.

Run processing pipeline by typing below (or clicking link) into command window (no semi-colon!):
obj`

I am trying to view a .avi file created using miniscope software. I am on a mac and have tried in matlab 2016b and 2018b. I keep getting the error:

Error using VideoReader/init (line 619)
Could not read file due to an unexpected error. Reason: Cannot Decode

I am able to open the video in VLC though not in quicktime. I thought perhaps it was an issue with matlab 2018b based on this thread but going down to 2016b also did not work. Any advice? Thanks!

Hi,Biafra
I'm following the steps of your video in youtube to run ciatah,but i have a error.
When viewMovieRegistrationTest is running,the following error occurs.

I don't know how to handle it. Would you help me find the problem? Looking forward to your reply.

Yancy

Hello,

I have been trying to preprocess a video, and in particular to apply motion correction to it (because I have done the other steps such as downsampling and spatially filtering it in the Inscopix Data Processing Software before exporting it as a .tiff file for motion correction and cell extraction) but I do not find the output .h5 file once the program runs turboreg (I have tried to save the motion corrected and the df/f movies) hence I can't further run cell extraction algorithms. Errors such as these appear :

Error using h5create (line 71)
The value of 'Dataset' is invalid. Expected DATASET to be nonempty.

Error in writeHDF5Data (line 74)
h5create(saveDir,options.datasetname,dataDims,'Datatype',inputClass,'ChunkSize',dataDimsChunkCopy,'Deflate',options.deflateLevel);

Error in calciumImagingAnalysis/modelPreprocessMovieFunction (line 645)
movieSaved = writeHDF5Data(thisMovie,savePathStr,'datasetname',options.outputDatasetName,'addInfo',{options.turboreg,analysisOptionStruct,optionsCopy},'addInfoName',{'/movie/processingSettings','/movie/analysisOperations','/movie/modelPreprocessMovieFunctionOptions'},'deflateLevel',options.deflateLevel)

Error in calciumImagingAnalysis/modelPreprocessMovie (line 37)
obj.modelPreprocessMovieFunction('folderListPath',folderListInfo,'fileFilterRegexp',options.fileFilterRegexp,'datasetName',options.datasetName,'frameList',[]);

Error in calciumImagingAnalysis/runPipeline (line 1582)
obj.(thisFxn{1});

Error in calciumImagingAnalysis/display (line 882)
obj.runPipeline;
@@@@@@@

I am new to this and not sure of what is causing this issue, what could I try to fix this?

Thanks a lot for your support and guidance,
Best wishes

Dear Biafra,

we are running Ciatah (latest version) on matlab 2020 and 2021, and turboreging the videos (.h5).
However, we manage to run it once correctly and then we ge the following error:

1/1: D:\favilan
SKIPPING ANALYSIS FOR THIS FOLDER
pre-allocating movies to display...
Miji loaded!

It seems to be skipping folders for some reason?
Could you help us?

Thanks!
Natalia

Hi Biafra,
After "modelVarsFromFiles", I'm trying to run computeMatchObjBtwnTrials, and get the following error:

I was successfully able to do this with the same data set just last week.. so I'm probably just making a stupid mistake. Any ideas what would cause this?

Omid

Hi Biafra,
I'm running MATLAB_2017b on Mac OS. I know you haven't tested on either of these, but I'm hoping there might be an easy solution.

I have downloaded the demo data to the path:
/omidd/calciumImagingAnalysis/data/2014_04_01_p203_m19_check01_raw, and typed that exact pathname in the window that opens up after you click ModelAddNewFolders.

When I then try to view the movie through the viewMovie module, a series of prompts (animal number, session number, etc) leads me to an open Finder window where I'm asked to open a file. I'm not sure what I'm supposed to open in this window. Is it the movie file? Unfortunately that seems to be greyed out. Does this mean I have not loaded the files correctly?

The error code I ultimately get is:

Miji has been set up correctly, because I can use the command MIJ.start.

Omid

Dear Biafra,

we are using Ciatah to analyse our Ca imaging data, but we are struggling finding good parameter values for the PCA-ICA cell extraction.
Can you tell me what the mu and term_tol paramters are? or point me towards any documentation or literature where they are explained?

Thank you!
Natalia

Hi, Biafra~

Lately, I've been working on a two-photon .tiff file through computeManualSortSignals on MatLab 2020b, win10. Normally, all things pretty good so far. Thank you for the update version2.5.1, it's amazing.

Could you please concretely enlighten a handy approach or code to help me to export the SNR value of every identified cell while or finishing the computeManualSortSignals part. I could only read it from the interface like below on-by-one.

If there is no misunderstanding on SNR here in CIAtah v2.5.1, that is Signals Noise Ratio, an important parameter I would use someday. So, hope you would help me with that.

And, one more thing, have you ever considered uploading a teaching video on the Internet about the rest of the operation after computeManualSortSignals?

Best Wishes to you!

Benson
from SheepMountain, NJ

Hi,
I remember reading something in a readme a while ago that there is a more exact way to get peak times than using extractedPeaks, but for the life of me I cannot find it anymore. Is it deprecated?

Thank you!

Line 415 in ciapkg.io.loadMovieList.m seems to have an extra line that needs to be commented out in the AVI case, or else AVIs will fail to load correctly. I commented out that line and everything ran smoothly.

case 'avi'
    xyloObj = VideoReader(thisMoviePath);
    dims.x(iMovie) = xyloObj.Height;
    dims.y(iMovie) = xyloObj.Width;
    dims.z(iMovie) = xyloObj.NumberOfFrames;
    dims.one(iMovie) = xyloObj.Height;
    dims.two(iMovie) = xyloObj.Width;
    dims.three(iMovie) = xyloObj.NumberOfFrames;
    tmpFrame = read(xyloObj, 1, 'native');
>   %tmpFrame = tmpFrame.cdata;
    %tmpFrame = readFrame(xyloObj);

Hi,
I just updated to the most up to date version of ciatah but upon running modelpreprocessMovie to preprocess a .tif movie we run in the error below. We are running in MATLAB R2021b
Let us know what could be the issue: the regex and video filename are corresponding (precisely 077_01, if this could in any way be the issue).

Running standard TIFF
@@@@@@@
Undefined function 'tiffread' for input arguments of type 'char'.

Error in ciapkg.io.load_tif_movie/standardTIFF_new (line 181)
            out.Movie = tiffread(filename,[],'ReadUnknownTags',1);

Error in ciapkg.io.load_tif_movie (line 85)
		standardTIFF_new();

Error in ciapkg.api.load_tif_movie (line 13)
	[out] = ciapkg.io.load_tif_movie(filename,downsample_xy,'passArgs', varargin);

Error in ciapkg.io.loadMovieList (line 643)
						outputMovie = load_tif_movie(thisMoviePath,1,'displayInfo',options.displayInfo,'fileInfo',fileInfoH);

Error in ciapkg.api.loadMovieList (line 9)
	[outputMovie, movieDims, nPixels, nFrames] = ciapkg.io.loadMovieList(movieList, 'passArgs', varargin);

Error in ciatah/modelPreprocessMovieFunction (line 814)
						thisMovie = loadMovieList(movieList,'convertToDouble',0,'frameList',thisFrameList,'inputDatasetName',options.datasetName,'treatMoviesAsContinuous',options.turboreg.treatMoviesAsContinuousSwitch,'loadSpecificImgClass','single','largeMovieLoad',options.turboreg.largeMovieLoad);

Error in ciatah/modelPreprocessMovie (line 42)
	obj.modelPreprocessMovieFunction('folderListPath',folderListInfo,'fileFilterRegexp',options.fileFilterRegexp,'datasetName',options.datasetName,'frameList',[]);

Error in ciatah/runPipeline (line 209)
				obj.(thisFxn{1});

Error in ciatah/display (line 6)
	obj.runPipeline;
@@@@@@@
+++++++
no movie!

Hi Biafra,

Some people in the lab are getting started with new imaging projects and have been using the calciumImagingAnalysis package with great success to preprocess movies and extract cells.
They've been using cnmf-e and I am a bit unsure about what should be used from the cnmfeAnalysisOutput file for further data analysis.
For example when I extract cells from movies for my project with Extract, I then use extractAnalysisOutput.traces. But cnmfeAnalysisOutput has extractedSignals, extractedSignalsEst, and extractedPeaks.

What is exactly the difference between these 3, and do you have any advice on what is best to use when one wants to plot rate maps for example?

Thanks!
Lucie

I tried to use the ciatah signalSorter function as specified here. However, I got an loop error.

It gives this warning at the start.

Warning: File: computeSignalSnr.m Line: 148 Column: 5
The temporary variable 'loopMean' will be cleared at the beginning of each
iteration of the parfor-loop. If 'loopMean' is used before it is set, a runtime
error will occur. For more information, see Parallel for Loops in MATLAB,
"Uninitialized Temporaries".
In signalSorter (line 413)

Then keeps repeating this error until it is stopped.

@@@@@@@
Index exceeds the number of array elements (2).

Error in compareSignalToMovie (line 101)
nPoints = options.inputMovieDims(3);

Error in signalSorter>viewMontage (line 2505)
croppedPeakImages = compareSignalToMovie(inputMovie, inputImage, thisTrace,'getOnlyPeakImages',1,'waitbarOn',0,'extendedCrosshairs',2,'crossHairVal',maxValMovie*options.crossHairPercent,'outlines',1,'signalPeakArray',signalPeakArray,'cropSize',cropSizeLength,'addPadding',1,'outlineVal',NaN,'xCoords',xCoords,'yCoords',yCoords,'inputDatasetName',options.inputDatasetName,'inputMovieDims',options.inputMovieDims,'hdf5Fid',options.hdf5Fid,'keepFileOpen',options.keepFileOpen);

Error in signalSorter>chooseSignals (line 986)
[objCutImagesCollection{i}, ~] = viewMontage(options.inputMovie,thisImage,options,thisTrace,[signalPeakIdx{i}],minValMovie,maxValMovie,options.cropSizeLength,i,1);

Error in signalSorter (line 603)
[choices, safeExit] = chooseSignals(options,1:nSignals, inputImages,inputSignals,objMap, valid, inputStr,tmpDir,sessionID,signalPeakIdx,signalSnr,inputImagesThres,inputImageSizes,peakOutputStat,ROItraces,imgStats,inputSignalSignal,inputSignalNoise,inputImagesBoundaryIndices,signalPeakIdxOriginal,signalPeaksOriginal,instructionStr);
@@@@@@@
@@@@@@@
Index exceeds the number of array elements (0).

Error in signalSorter>chooseSignals (line 1046)
title(['imageCorr = ' num2str(round(peakOutputStat.outputMeanImageCorrs(i)*sigDig)/sigDig) 10 'Press Y to go to last sorted signal.'],'FontSize',options.fontSize,'Interpreter','tex');

Error in signalSorter (line 603)
[choices, safeExit] = chooseSignals(options,1:nSignals, inputImages,inputSignals,objMap, valid, inputStr,tmpDir,sessionID,signalPeakIdx,signalSnr,inputImagesThres,inputImageSizes,peakOutputStat,ROItraces,imgStats,inputSignalSignal,inputSignalNoise,inputImagesBoundaryIndices,signalPeakIdxOriginal,signalPeaksOriginal,instructionStr);
@@@@@@@
0 0
cellmap type: max
@@@@@@@
Index exceeds the number of array elements (0).

Error in signalSorter>chooseSignals (line 1279)
' | imageCorr = ' num2str(round(peakOutputStat.outputMeanImageCorrs(i)*sigDig)/sigDig) ',' num2str(peakOutputStat.outputMeanImageCorrs2(i))...

Error in signalSorter (line 603)
[choices, safeExit] = chooseSignals(options,1:nSignals, inputImages,inputSignals,objMap, valid, inputStr,tmpDir,sessionID,signalPeakIdx,signalSnr,inputImagesThres,inputImageSizes,peakOutputStat,ROItraces,imgStats,inputSignalSignal,inputSignalNoise,inputImagesBoundaryIndices,signalPeakIdxOriginal,signalPeaksOriginal,instructionStr);
@@@@@@@
All warnings have the state 'off'.
calculating movie min/max...
finding centroids...
Finding cell neighbors: 10|100
Done assigning neighbor IDs...

ans =

'Frame 1/4000'

@@@@@@@

Dear Biafra,

is there a way to merge two components into one? We are using PCA-ICA and some cells are segmented into "subcells" that we would like to merge together so that it is only one cell.

Thank you!
Natalia

Hey Biafra!
I am running computeMatchObjectsbtwSessions on a new data set and encountering that error that you previously fixed, something about dividing by zeros after CNMF-e?

Omid

Hi,

after some hours of trying to get Ciatah to run, I installed it anew by cloning it from github with matlab and decided to ask for help. I wanted to test varius functions of Ciatah and use it for cellextraction from 1photon miniscope data.

I started by using the function modelDownsampleRawMovies. After the input GUI it returns following error message.

I tried the function viewMovieRegistrationTest and get the same error message. I am running Matlab2020b, all dependencies are loaded correctly, as it is stated when starting up Ciatah.

Where is my mistake? any help is appreciated

Regards

Hi Biafra,

I'm trying to run CIAtah 4.0 on MATLAB R2020b, on a windows.
but i even cant install it well.
I cant find the file cvx_setup.m (likely calcuumagingAnalysis/_external_programs/cvx_rd).

Hi Biafra,
Super excited that the new cell extraction method is released and supported by CIAtah!
I was able to load EXTRACT into the external_programs folder, but under Cell Extraction Methods in the GUI, the only "EXTRACT" is still the 2017 version. Is this the correct method?
Omid

Upgraded to the new version of CIATAH and now I get "Please input a file path." during preprocess movie. Everything is the same as how I have done it in other versions....

Running: obj.modelPreprocessMovie
Loading MIJI + ImageJ.
Adding to Java path: C:\Users\HomePC\OneDrive - Northwestern University\Documents\ciatah-master\_external_programs\imagej\mij.jar
Warning: Invalid file or directory 'C:\Users\HomePC\OneDrive - Northwestern
University\Documents\ciatah-master\_external_programs\imagej\mij.jar'. 
> In javaclasspath>local_validate_dynamic_path (line 271)
In javaclasspath>local_javapath (line 187)
In javaclasspath (line 124)
In javaaddpath (line 71)
In ciapkg.io.manageMiji (line 122)
In ciapkg.api.manageMiji (line 10)
In ciapkg.io.modelAddOutsideDependencies (line 43)
In ciapkg.api.modelAddOutsideDependencies (line 10)
In ciatah/modelPreprocessMovie (line 21)
In ciatah/runPipeline (line 209)
In ciatah/display (line 6) 
Loading MIJI + ImageJ.
Adding to Java path: C:\Users\HomePC\OneDrive - Northwestern University\Documents\ciatah-master\_external_programs\imagej\ij.jar
Warning: Invalid file or directory 'C:\Users\HomePC\OneDrive - Northwestern
University\Documents\ciatah-master\_external_programs\imagej\ij.jar'. 
> In javaclasspath>local_validate_dynamic_path (line 271)
In javaclasspath>local_javapath (line 187)
In javaclasspath (line 124)
In javaaddpath (line 71)
In ciapkg.io.manageMiji (line 122)
In ciapkg.api.manageMiji (line 10)
In ciapkg.io.modelAddOutsideDependencies (line 43)
In ciapkg.api.modelAddOutsideDependencies (line 10)
In ciatah/modelPreprocessMovie (line 21)
In ciatah/runPipeline (line 209)
In ciatah/display (line 6) 
                   matfilePath: ''
                matfileVarname: 'thisMovie'
                    runMatfile: 0
                   showFigures: 1
                folderListPath: {'C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope'}
       checkConcurrentAnalysis: 1
    concurrentAnalysisFilename: '_currentlyAnalyzingFolderCheck.mat'
       processMoviesSeparately: 0
                 processMovies: 1
           loadOptionsFromFile: 0
       turboregNumFramesSubset: 3000
                  turboregType: 'preselect'
                      turboreg: [1×1 struct]
                     dfofMovie: 1
                      dfofType: 'dfof'
              downsampleFactor: 4
                      pxToCrop: 14
              fileFilterRegexp: 'concat_.*.h5'
                   inputPCAICA: 0
                   askForPCICs: 0
                     frameList: []
                   datasetName: '/1'
             outputDatasetName: '/1'
                  refCropFrame: 1
                  deflateLevel: 1
                supportedTypes: {'.h5'  '.hdf5'  '.tif'  '.tiff'  '.avi'  '.isxd'}
    calcDroppedFramesFromMovie: []
                       minType: 'soft'
                    minSoftPct: 1.0000e-03
                    saveMovies: 0
                 saveDfofMovie: 0
                 turboregMovie: 1
                normalizeMovie: 0
               downsampleMovie: 1
                 logFileRegexp: '(recording.*.(txt|xml)|.*_metadata.mat)'
        nwbSettingsDatasetname: '/general/optophysiology/imaging_plane/description'
         h5SettingsDatasetname: '/movie/preprocessingSettingsAll'
                saveFilePrefix: ''
                saveFileSuffix: ''
                   videoPlayer: 'matlab'


ans =

     1

Warning: The DrawMode property will be removed in a future release. Use the SortMethod property instead. 
> In inputdlg (line 258)
In ciatah/modelPreprocessMovieFunction (line 487)
In ciatah/modelPreprocessMovie (line 42)
In ciatah/runPipeline (line 209)
In ciatah/display (line 6) 
    {0×0 char}
    {'raw'   }
    {'/1'    }
    {'/1'    }
    {'1'     }
    {'0'     }
    {0×0 char}
    {0×0 char}
    {'matlab'}
    {0×0 char}


ans = 

  struct with fields:

                           MAIN______________: [1×1 struct]
                      checkConcurrentAnalysis: [1×1 struct]
                            resetParallelPool: [1×1 struct]
                              analyzeFromDisk: [1×1 struct]
                   calcDroppedFramesFromMovie: [1×1 struct]
                   REGISTRATION______________: [1×1 struct]
                                     parallel: [1×1 struct]
                              registrationFxn: [1×1 struct]
                             turboregRotation: [1×1 struct]
                                    RegisType: [1×1 struct]
                        numTurboregIterations: [1×1 struct]
                      turboregNumFramesSubset: [1×1 struct]
                                     pxToCrop: [1×1 struct]
                     motionCorrectionRefFrame: [1×1 struct]
     REGISTRATION_NORMALIZATION______________: [1×1 struct]
                        normalizeMeanSubtract: [1×1 struct]
               normalizeMeanSubtractNormalize: [1×1 struct]
                    normalizeComplementMatrix: [1×1 struct]
                                normalizeType: [1×1 struct]
                             normalizeFreqLow: [1×1 struct]
                            normalizeFreqHigh: [1×1 struct]
                        normalizeBandpassType: [1×1 struct]
                        normalizeBandpassMask: [1×1 struct]
                                      SmoothX: [1×1 struct]
                                      SmoothY: [1×1 struct]
                                      zapMean: [1×1 struct]
            MOVIE_NORMALIZATION______________: [1×1 struct]
                         filterBeforeRegister: [1×1 struct]
                     saveBeforeFilterRegister: [1×1 struct]
                     saveFilterBeforeRegister: [1×1 struct]
                       filterBeforeRegFreqLow: [1×1 struct]
                      filterBeforeRegFreqHigh: [1×1 struct]
                filterBeforeRegImagejFFTLarge: [1×1 struct]
                filterBeforeRegImagejFFTSmall: [1×1 struct]
                             medianFilterSize: [1×1 struct]
             MOVIE_DOWNSAMPLING______________: [1×1 struct]
                         downsampleFactorTime: [1×1 struct]
                        downsampleFactorSpace: [1×1 struct]
    IO_and_MOVIE_IDENTIFICATION______________: [1×1 struct]
                             inputDatasetName: [1×1 struct]
                            outputDatasetName: [1×1 struct]
                             fileFilterRegexp: [1×1 struct]
                      processMoviesSeparately: [1×1 struct]
                       loadMoviesFrameByFrame: [1×1 struct]
                treatMoviesAsContinuousSwitch: [1×1 struct]
                        loadMovieInEqualParts: [1×1 struct]
                                  useParallel: [1×1 struct]
                             nParallelWorkers: [1×1 struct]
                 STRIPE_REMOVAL______________: [1×1 struct]
                       stripOrientationRemove: [1×1 struct]
                                    stripSize: [1×1 struct]
                          stripfreqLowExclude: [1×1 struct]
                         stripfreqHighExclude: [1×1 struct]
                        stripfreqBandpassType: [1×1 struct]


ans =

     1

:
                           MAIN______________: {'====================='}
                      checkConcurrentAnalysis: 0
                            resetParallelPool: 0
                              analyzeFromDisk: 0
                   calcDroppedFramesFromMovie: []
                   REGISTRATION______________: {'====================='}
                                     mcMethod: 'turboreg'
                                     parallel: 1
                              registrationFxn: 'transfturboreg'
                             turboregRotation: 0
                                    RegisType: 1
                        numTurboregIterations: 1
                      turboregNumFramesSubset: 5000
                                     pxToCrop: 14
                     motionCorrectionRefFrame: 100
                     regRegionUseBtwnSessions: 1
     REGISTRATION_NORMALIZATION______________: {'====================='}
                        normalizeMeanSubtract: 1
               normalizeMeanSubtractNormalize: 1
                    normalizeComplementMatrix: 1
                                normalizeType: 'bandpass'
                             normalizeFreqLow: 70
                            normalizeFreqHigh: 100
                        normalizeBandpassType: 'bandpass'
                        normalizeBandpassMask: 'gaussian'
                                      SmoothX: 10
                                      SmoothY: 10
                                      zapMean: 0
            MOVIE_NORMALIZATION______________: {'====================='}
                         filterBeforeRegister: []
                     saveBeforeFilterRegister: 0
                     saveFilterBeforeRegister: []
                       filterBeforeRegFreqLow: 0
                      filterBeforeRegFreqHigh: 10
                filterBeforeRegImagejFFTLarge: 10000
                filterBeforeRegImagejFFTSmall: 80
                             medianFilterSize: 3
                  MOVIE_DETREND______________: {'====================='}
                                detrendDegree: 1
             MOVIE_DOWNSAMPLING______________: {'====================='}
                         downsampleFactorTime: 2
                        downsampleFactorSpace: 3
    IO_and_MOVIE_IDENTIFICATION______________: {'====================='}
                             inputDatasetName: '/1'
                            outputDatasetName: '/1'
                             fileFilterRegexp: 'raw'
                      processMoviesSeparately: 0
                       loadMoviesFrameByFrame: 0
                treatMoviesAsContinuousSwitch: 1
                        loadMovieInEqualParts: 0
                                  useParallel: 1
                             nParallelWorkers: 11
                               largeMovieLoad: 0
                 STRIPE_REMOVAL______________: {'====================='}
                       stripOrientationRemove: 'none'
                                    stripSize: 7
                          stripfreqLowExclude: 20
                         stripfreqHighExclude: 20
                        stripfreqBandpassType: 'highpass'
                                 refCropFrame: 100

Saving settings to: C:\Users\HomePC\OneDrive - Northwestern University\Documents\ciatah-master\private\settings\20230419_004031_modelPreprocessMovieFunction_settings.mat.
folderListMinusComments class: double
1/1: C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope
options.fileFilterRegexp: raw
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(1).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(2).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(3).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(4).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(5).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(6).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(7).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(8).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(9).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(10).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(11).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(12).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(13).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(14).avi
C:\Users\HomePC\OneDrive - Northwestern University\Desktop\videos\eyeblink\022223\2023_04_18\19_01_33\My_V4_Miniscope\raw(15).avi
Please input a file path.
>> `

Hello,
I'm having an issue when I try to save my results from the cross-session cell alignment. When I try using modelSaveMatchObjBtwnTrials a gui pops up for me to select a folder to save my data. After having selected a folder then this pops up

The issue is that when I try to look through the folder that I selected to save my data then the file is not there. How can I save the data, and how can I access the file?

Dear Biafra,

we are wondering if it would be possible to deploy ciatah for batch processing in a high performance computing cluster?
Is this something that you have done before or have any experience with?

We have large videos and even with temporal (to 5 Hz) and spatial (4x) downsampling, the process is using up our RAM (of around 300 GB).

Any other suggestion is also welcome!

Thank you!
Natalia

As mentioned on https://imagej.net/plugins/miji, this legacy project is mostly replaced by the functionality in ImageJ-MATLAB:

https://imagej.net/scripting/matlab#running-imagej2-within-matlab

I don't know the usage of Miji in ciatah in detail, and I don't know how involved a transition would be, but it might simplify it for users to just enable the ImageJ-MATLAB update site in Fiji (especially since the Miji website seems to be offline at the moment).

I know that @kouichi-c-nakamura worked quite a bit with the ImageJ-MATLAB integration, he might be able to give helpful advice.

Hi, I am batch converting many isxd movies to h5 via the command line. Is there an option to specify a path to the Inscopix software installation in my script?

import ciapkg.inscopix.*
import ciapkg.image.*
import ciapkg.api.*

file_name = strcat(root_dir, '/ISXD_files/', arg1);
opts.maxChunkSize = 5000;
opts.downsampleFactor = 1;
opts.baseInscopixPath = strcat('path_to_inscopix/MATLAB'); % <----
opts.saveFolder = strcat(root_dir, '/HDF5');
convertInscopixIsxdToHdf5(file_name,'options',opts);

Hi @bahanonu , I was analyzing video and do see drift in delta F/F. Do you have any idea why is that?
I am not sure, but it looks like this mouse show some transients. What do you think?

Thanks!

A bunch of warnings pops up as soon as I open it. The command line font is adjusted very small, and there are a lot of garbled characters. The font of the graphical interface is instead too large, causing the display to be truncated.
This extremely terrible GUI makes my first impression very bad, and now I have no desire to use it at all.
I recommend that if the GUI is not well done, don't show it, and honestly do a pure codeful API.

I have a bigTIFF video and have ran downsampling, motion correction, df/f, followed by CNMF-E (saved in .NWB format). I'm not sure how to correctly run viewCellExtractionOnMovie to obtain something like what's in the step-by-step guide where the outlines of extracted cells are superimposed on the video. When I run it via the GUI, I can get the video to display but there aren't any outlines. The .NWB output of CNMF-E is in the same folder as the video. Any help is appreciated!

I am getting cell segmentations that look pretty bad, and I think it might be because of how I am preparing the videos. Screenshots of the cell segmentations on the raw bigTIFF video and the preprocessed (downsampled 4x, turbo-reg'd, dfof) video are below:

Raw:

Pre-processed

I think the problem might be how I am preparing the bigTIFF video. The video is prepared from TIF images using the following script:

import cv2
import os
import numpy as np
from tqdm import tqdm
from tifffile import *

def tif_to_video(input_path, output_filename):

    # Define the location of the TIF files
    dir_path = f'{input_path}'

    # List of TIF files
    tif_files = [f for f in os.listdir(dir_path) if f.endswith('.TIF')]

    # Sort image filenames by number following 'p' in filename
    framenums = []
    for tif_file in tif_files:
        p_idx = tif_file.find('p')
        underscore_idx = tif_file[p_idx:].find('_')
        framenum = tif_file[p_idx+1:p_idx+underscore_idx]
        framenums.append(int(framenum))
    
    # order filenames in a list
    tif_files = [tif_file for _, tif_file in sorted(zip(framenums, tif_files))]

    ### bigTIFF ###
    output_file = f'{output_filename}.tif'

    arr_list = []
    # Iterate over the TIF files, import and add each TIF frame to arr_list
    for i, tif_file in tqdm(enumerate(tif_files)):
        img = cv2.imread(os.path.join(dir_path, tif_file), 0)
        img = img[...,None] # add third dimension (i.e., frame)
        arr_list.append(img)
    
    # concatenate frames into numpy array
    tiff_arr = np.concatenate(arr_list, axis=2)
    
    # export numpy array in bigTIFF format at 20 FPS
    with TiffWriter(output_file, bigtiff=True) as tif:
        for frame in np.transpose(tiff_arr,(2,0,1)):
            tif.write(frame, metadata={'fps':20.0}, compression='JPEG')    

Any help with this is greatly appreciated. Thanks in advance!

Hi Guys,
First of all, thanks a lot for your hard work.
I am working with peculiar videos and running ciatah for motioncorr and EXTRACTing calcium data separately to fine tune parameters for cell finding and refinement.
I then would like to use signalSorter but it looks like it's not there in the repo. I hope I am not doing something stupid :') and thank you in advance for your help!!

Correction: it is in the ciapkg folder of the cloned repo so i guess it's just a problem on my side... Thanks anyways and sorry for bothering

Antonio