search

wiggins-lab / SuperSegger

A completely automated MATLAB-based trainable image cell segmentation, fluorescence quantification and analysis suite, particularly well suited for high-throughput time lapse fluorescence microscopy of in vivo bacterial cells.
GNU General Public License v3.0
32 stars 20 forks source link

bwlabel error #12

Closed showmepuppies closed 6 years ago

showmepuppies commented 6 years ago

Hi! I am segmenting E. coli cells and would like to modify the constants to get better results.

However, I am getting a persistent error message when using trainingGui:

Error using bwlabel Expected input number 1, BW, to be two-dimensional.

What is happening here? FYI the segmentation process itself runs without errors, I am only getting this problem in the training section.

sharsnik commented 6 years ago

Please upload the image files (or .seg files) you are attempting to train on. Along with a screenshot of the training menu just before the error occurs.

On Fri, May 4, 2018 at 11:59 AM, showmepuppies notifications@github.com wrote:

Hi! I am segmenting E. coli cells and would like to modify the constants to get better results.

However, I am getting a persistent error message when using trainingGui:

Error using bwlabel Expected input number 1, BW, to be two-dimensional.

What is happening here? FYI the segmentation process itself runs without errors, I am only getting this problem in the training section.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/wiggins-lab/SuperSegger/issues/12, or mute the thread https://github.com/notifications/unsubscribe-auth/ACgQ7hS_7N9HpNMH_woQyj-hkjhqYBY2ks5tvHrzgaJpZM4Ty5BI .

-- -Connor Brennan Fractal Entertainment www.side-quest.com

showmepuppies commented 6 years ago

I figured it out, the images were still RGB, after converting them to 8-bit the error disappeared. Thanks! Strange though that the segmentation process didn't complain about this, only the training bits.

pawiggins commented 6 years ago

showmepuppies:

I added code to flatten the RGB images to grayscale in all the parts of SS (I think).

--PAW