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LieberInstitute / dotdotdot

Example vignette for dotdotdot software
GNU Affero General Public License v3.0
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Trouble with implementing RNAscope function for humans #13

Open balajiisawesome opened 2 years ago

balajiisawesome commented 2 years ago

Hi, I am currently working through the tutorial for implementing Dotdotdot for human RNAscope data. However, after assigning the MATLAB and czi files to variables (as shown in the tutorial), I try to run the rnascope_human function, but it says the function is not recognized.

So instead, I assigned rnascope_human to the pathway leading to the rnascope_human.m file within my toolbox folder, but now when I run rnascope_human(filename, toolbox, DAPI, LIP, DROP), I am getting an error that says "Index in position 1 exceeds array bounds (must not exceed 1)." Because I am relatively new to MATLAB, I am not sure how to resolve this issue. Please let me know next steps for how to fix this issue and continue using Dotdotdot. This is a great software that I think really helps scientists everywhere.

Attached is an image depicting the problems above; please look at the code from the 1/3 from the top of the command window: Screen Shot 2021-09-07 at 1 26 53 PM

Any help is much appreciated! I really want to use this software and learn more about this cutting-edge technology.

Regards, Balaji

madhavitippani commented 2 years ago

Can you make sure the path you provided to the toolbox is correct and also if you successfully downloaded the entire package. This seems to be that MATLAB is not able to find the rnascope_human function in your specified toolbox directory.

balajiisawesome commented 2 years ago

Hello, Thank you for your response. I downloaded the entire package, but only put the toolbox in my working folder. Is that the problem? Do I need to put the whole package inside my working folder? I did not assume so because the rnascope_human.m file was within the toolbox function, which was kept inside my working folder.

For the path, I got the path of the toolbox directory from a terminal window, and then copied and pasted the path into MATLAB. I tried many times to redo the path, but I got the same error.

I will try putting the whole package inside my directory. If there is another error that I should I focus on, please let me know. I will get back to you shortly.

Thank you for your help so far, Balaji