MatLab TiffRead Error

[calvinthommek]

Hello,
I'm a student from Heidelberg and we wanted to try out your program in our lab.
When trying to run the program in math lab there comes an error because of the tiffRead function.
Is there any manual on how to run this program? It's really confusing to set it up when not having much experience with Python or MatLab.
Would be really nice if you could help with getting this program run.
Kind regards,
Calvin Thommek

[sautami26]

Hello,
Even I tried to run your program but it gives an error because of the tiffRead function.
I would also request you if you could help with resolving this error and getting the program run.
Regards
Sautami

[cihanbilge]

All necessary files are in my other respiratory: https://github.com/cihanbilge/SomaExtraction These are connected projects so there are a few common functions. tiffread.m and conncomp.m are the ones you can find in SomaExtraction respiratory. Of course I do my best to help. I am mostly busy with classes and projects so could be back late. But still I will try to help with anything about the code and/or method. sautami26 <[email protected]>, 8 Tem 2020 Çar, 22:29 tarihinde şunu yazdı:

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Hello, Even I tried to run your program but it gives an error because of the tiffRead function. I would also request you if you could help with resolving this error and getting the program run. Regards Sautami — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE33FFCG3DUOENABLZHC6GDR2TCKZANCNFSM4LX3UIOQ> .

[sautami26]

Hello Sir,
Thank you very much for your response. I totally understand your busy schedule and despite that you could spare some time and responded, I am highly obliged.
I am a PhD student, new to this deep learning domain. Hence, I require guidance sometimes when I get stuck.
Today on seeing your response I could run that part of the code. Now, I got stuck with the 'sm' variable (code snippet below). I tried to figure it out for quite a long time but no luck.
%to catch the cells close to the boundry efficiently we zero-pad the image and Directional Ratio from each side
imagebase=zeros(max(size(image))+subimage_size);
side=subimage_size/2;
imagebase(side:side-1+sm(1), side:side-1+sm(2))=DirectionalRatio;
DirectionalRatio=imagebase;
imagebase=zeros(sm_max+subimage_size);
imagebase(side:side-1+sm(1),side:side-1+sm(2))=image;
image=imagebase;

Can you please guide me in resolving this issue.

Regards
Sautami

[skenney1652]

Hello,

I'm having an identical issue to Sautami when running the Matlab script astrocytes_dataGeneration. It looks like the variable sm isn't defined, when using CTRL+f, I find the first instance of that variable in this line:
imagebase(side:side-1+sm(1),side:side-1+sm(2))=DirectionalRatio;. It looks like maybe in some edition of the code it was previously defined but maybe didn't make it to the script uploaded in this package.

I haven't reached this line yet but it looks like we'll have the same issue with the variable sm_max which first appears in this line: imagebase=zeros(sm_max+subimage_size);
Could you load a version of the script including these elements defined? Similar to Sautami I'm not sure how to reason my way to defining them myself so it would be great if you could send something.

Another issue I was having was specifying image_list for just loading the data by tiffRead. I tried using the names of the files you included in the SomaExtraction package, e.g. MAX_24h_CHIR99021_FGF14_488_PanNav_568_MAP2_647_10_blue, but this doesn't work. To get things going, I just bypassed all this and manually tif-read the images myself but I feel like your design is probably more efficient, I just want to know how to use it. It's not terribly clear from the comments, at least to me. That's all I have for now, thank you for uploading the code for this really neat method and for answering our questions. I'm looking forward to running it on the data I'm studying. Thanks!

Best,
Steven

[bpavie]

Same issue as @sautami26 and @skenney1652 , after having added the function tiffRead.m from https://github.com/cihanbilge/SomaExtraction and re-run the script we can see that the variable sm is never set (and if it is a function it is not available), do we need to declare it somewhere?

Best,
Benjamin