search

usnistgov / FogBank

Single Cell Segmentation
Other
12 stars 6 forks source link

Seed Image Dimension Mismatch #1

Open Nicholas-Schaub opened 6 years ago

Nicholas-Schaub commented 6 years ago

I am trying to segment multiple stitched images at the same time. I am trying to use a segmented image of nuclei as the initial seed positions. Although the dimensions of the image to be segmented and the nuclei seed image are the same for a particular image, the dimensions of each image to be segmented are not the same. The preview for the labeled image looks fine for the first image, but then if I try to preview the second image I get either a size error or index exceeds dimension error. I get the same error when I try to process and save all of the images.

I haven't dug into the code, but I assume this error could be caused by the program assuming all seed images are the same size.

mmajurski commented 6 years ago

Nick, Does your error happen on the latest version of the code from USNISTGOV Fogbank? I tried to reproduce this error using a few differently sized images I created using padding of a common starting image and I was unable to force the error.

Could you determine if this error happens when using a clone of the latest USNISTGOV Fogbank repo? Or could you send me some test data that causes the error?

Thanks, Michael

Nicholas-Schaub commented 6 years ago

Hi Mike,

I just cloned within the last month, and I haven't seen any recent updates.

I can send you some test data. I didn't try to reproduce the preview errors I got before, but I just ran it now and when I go to save the images I get the following error:

Error using fog_bank_perctile_geodist_seed (line 40)
Invalid <seed_image> wrong size

Error in FogBank_GUI/fogbank_given_image (line 2830)
  [segmented_image, ~] = fog_bank_perctile_geodist_seed(I1, logical(foreground_mask),
  ~temp_border_mask, seed_mask, min_object_size, fogbank_dir, prctile_bin);

Error in FogBank_GUI/save_images (line 1340)
      [segmented_image, nb_obj] = fogbank_given_image(frames_to_save(i));

Error in FogBank_GUI/save_images_GUI_callback/save_callback (line 1222)
  save_images(save_image_format, save_common_name, save_range, type_format);

Error while evaluating UIControl Callback.

I'll zip the images and send along.

Nick