search

LieberInstitute / dotdotdot

Example vignette for dotdotdot software
GNU Affero General Public License v3.0
18 stars 11 forks source link

Unable to run the code #5

Closed yoser-alrawi closed 4 years ago

yoser-alrawi commented 4 years ago

Hi, I am new to MATLAB and I have been trying to use the rnascope_mouse script. I tried using the raw image that was posted over here "Mouse2.czi" but I was still unable to run the code. What I did was that I downloaded the toolbox and put .czi image and associated .jpg images that I found in over here in the same folder as the toolbox. Then, I opened the rnascope_mouse.m script and changed the filename definition to the path that I was using and I did the same thing for the toolbox. Then I tried running the code but I kept getting errors with the input or with some parts of the script as shown in the screenshot.

Screen Shot 2020-07-22 at 11 37 56 PM

I am not sure whether there are some errors in the code or I am not doing things correctly.

vjysd commented 4 years ago

Hi Yoser,

Thank you for posting your issue. I suspect that you are executing the function rnascope_mouse.m instead of calling it. I suggest you try this and let me know if you're still having issues,

After navigating to the folder that has rnascope_mouse.m script, in the command window execute rnascope_mouse(YOUR_FILENAME_PATH, YOUR_TOOLBOX_PATH). Keep the first two commented lines that start with % as is. They are just for reference.

yoser-alrawi commented 4 years ago

Hi Vijay, Thank you for the reply! I have tried your suggestion and that helped but I was getting the following error :

"segmenting DAPI Error using rnascope_mouse (line 52) Error: This statement is incomplete."

Line 52 is "ch = eval(['img.',char(O(d))]); "

yoser-alrawi commented 4 years ago

An update: I was able to solve this issue by removing "%" at the beginning of line 20!

vjysd commented 4 years ago

Hi Yoser,

I'm glad it worked out.

yoser-alrawi commented 4 years ago

Thanks Vijay!