Grand Challenge

Try-out Algorithm error ¶

By: tle1302 on April 3, 2024, 8:01 a.m.

I created a (locally working) docker image that would take this example input : /input/images/organelles-transmitted-light-ome-tiff/image_196_DIC_z2.ome.tiff

and output these 4 ome.tiff:

/output/images/mitochondria-fluorescence-ome-tiff/image_196_DIC_z2.ome.tiff
/output/images/actin-fluorescence-ome-tiff/image_196_DIC_z2.ome.tiff
/output/images/nucleus-fluorescence-ome-tiff/image_196_DIC_z2.ome.tiff
/output/images/tubulin-fluorescence-ome-tiff/image_196_DIC_z2.ome.tiff

However, after uploading the container to grand challenge Algorithms, I can't "Try-out Algorithm". I tried uploading some ome.tiff from the training set, and the only error message is Job can't be started, input is missing for Organelles Transmitted-Light OME-TIFF. This is the upload error.

What can I do to debug this problem?

Last edited by: tle1302 on April 3, 2024, 8:31 a.m., edited 1 time in total.

Re: Try-out Algorithm error ¶

By: dorian_kauffmann on April 3, 2024, 9:09 a.m.

Hi,

I'm not sure to understand your error. I do the same as you in the Try-out-Algorithm section and load the same image - the one of your upload error - image_2486_PC_z12.ome.tiff.
The import was good as you can see:

And then I got a result :

How did you make your import ?
Is your algorithm docker working on every image as you talk about image_196_DIC_z2.ome.tiff and got an error with image_2486_PC_z12.ome.tiff?

Re: Try-out Algorithm error ¶

By: john.fozard on April 3, 2024, 10:28 a.m.

I'm getting the same error with an image uploaded via the webform:

TIFF image builder: Could not open file with tifffile. TIFF image builder: Validation error: Not a valid tif: Voxel width could not be determined.

I'm using Chrome on Linux

John

Re: Try-out Algorithm error ¶

By: tle1302 on April 3, 2024, 11:06 a.m.

I figured out that the upload would work for files that are downloaded from source again. All local files opened in Fiji somehow failed.

Re: Try-out Algorithm error ¶

By: dorian_kauffmann on April 3, 2024, 12:14 p.m.

Could you be more precise? With this little information, I'm sorry but, I can't understand the problem.

What image are you trying to load? What is the image uploaded via the webform? What do you mean by 'webform' ?

If you tried putting images in Docker, Then it's not the principle.

Re: Try-out Algorithm error ¶

By: john.fozard on April 3, 2024, 12:51 p.m.

Exactly like tle1302's error - attempting to test the algorithm (https://grand-challenge.org/algorithms/simple-unet/jobs/create/) fails for some images image_120_DIC_z8.ome.tiff uploaded using the "Upload a new image" option on that page.

The fix seems to be the same as suggested by tle1302 - download the images again from the database. I must have accidentally modified the file when viewing in Fiji.

Thanks for your help.