403 error when uploading a file using StomaAI, probably missing configuration file

[thrser]

This image is the result after uploading.
下面的图片是我上传我的样品图片后的结果

The detailed error reporting code is in the ppt
详细的报错代码在ppt中
StomaAI使用报错.pptx

I hope the teacher can help me to find the problem, whether the address of the configuration file is outdated, thank you very much.
希望老师能帮忙找找问题所在，是否是配置文件地址过期，非常感谢。

[thrser]

HTTPError: HTTP Error 403: Forbidden Traceback: File "/cluster/home/tanghuai/miniconda3/envs/SAI2/lib/python3.8/site-packages/streamlit/runtime/scriptrunner/exec_code.py", line 88, in exec_func_with_error_handling result = func() File "/cluster/home/tanghuai/miniconda3/envs/SAI2/lib/python3.8/site-packages/streamlit/runtime/scriptrunner/script_runner.py", line 579, in code_to_exec exec(code, module.dict) File "/cluster/home/tanghuai/softwares/stomaAI/SAI-app/src/main.py", line 38, in main() File "/cluster/home/tanghuai/softwares/stomaAI/SAI-app/src/main.py", line 16, in main maybe_do_inference() File "/cluster/home/tanghuai/softwares/stomaAI/SAI-app/src/app/inference.py", line 37, in maybe_do_inference maybe_do_single_image_inference() File "/cluster/home/tanghuai/softwares/stomaAI/SAI-app/src/app/inference.py", line 46, in maybe_do_single_image_inference predictions, time_elapsed = run_on_image(image) File "/cluster/home/tanghuai/softwares/stomaAI/SAI-app/src/inference/infer.py", line 32, in run_on_image maybe_setup_inference_engine() File "/cluster/home/tanghuai/softwares/stomaAI/SAI-app/src/inference/infer.py", line 43, in maybe_setup_inference_engine setup_inference_engine(selected_species) File "/cluster/home/tanghuai/softwares/stomaAI/SAI-app/src/inference/infer.py", line 47, in setup_inference_engine maybe_download_config_files(selected_species) File "/cluster/home/tanghuai/softwares/stomaAI/SAI-app/src/inference/infer.py", line 58, in maybe_download_config_files download_and_save_yaml(url, filename) File "/cluster/home/tanghuai/softwares/stomaAI/SAI-app/src/tools/load.py", line 33, in download_and_save_yaml save_yaml(filename, download_yaml(url)) File "/cluster/home/tanghuai/softwares/stomaAI/SAI-app/src/tools/load.py", line 37, in download_yaml with urllib.request.urlopen(url) as response: File "/cluster/home/tanghuai/miniconda3/envs/SAI2/lib/python3.8/urllib/request.py", line 222, in urlopen return opener.open(url, data, timeout) File "/cluster/home/tanghuai/miniconda3/envs/SAI2/lib/python3.8/urllib/request.py", line 531, in open response = meth(req, response) File "/cluster/home/tanghuai/miniconda3/envs/SAI2/lib/python3.8/urllib/request.py", line 640, in http_response response = self.parent.error( File "/cluster/home/tanghuai/miniconda3/envs/SAI2/lib/python3.8/urllib/request.py", line 569, in error return self._call_chain(*args) File "/cluster/home/tanghuai/miniconda3/envs/SAI2/lib/python3.8/urllib/request.py", line 502, in _call_chain result = func(*args) File "/cluster/home/tanghuai/miniconda3/envs/SAI2/lib/python3.8/urllib/request.py", line 649, in http_error_default raise HTTPError(req.full_url, code, msg, hdrs, fp)

[XDynames]

Yeah I agree it looks like the figshare hosting is not able to download that file. I can look into this when I have time.

If you are comfortable uploading your samples you can use the free hosted version we’ve been working on here: https://sai.plantphenomics.org.au/

[thrser]

Thank you very much, I will use the free hosted version developed by your team, you are a respectable scientist!

[thrser]

I uploaded my image but got a blank result.

image name,number of stomata,density,g max
6320006-1,0,0.0,0.0

May I ask what this is about?extremely grateful

[XDynames]

I downscaled the resolution to that which is recommend on the job submission page (2880x2048) and exported the sample 6320006-1 to png and it does pick up some stomata:

I don't know for sure how you gathered the images but the samples we use tend to be without the green staining and a little bit more in focus. For Example:

[thrser]

Thank you for your suggestion, our pictures are taken directly from untreated wheat leaves, so there is still some of the green color of the leaf pulp cells. Was your sample fixed and decolorized?

[XDynames]

Hmmm good question, in our paper it states: “ fresh epidermal peels were used as plant materials for image capture”

Perhaps our bioinformatician can shed some light? @CharlotteSai

[CharlotteSai]

Hi @thrser ,

To answer your question, first, we captured barley images with fresh barley epidermal peels. Methods of the peeling technique is described HERE. The raw image is NOT decolonised as @XDynames showed images above. There are still some green residual shown and some peels have mesophyll cells attached. See below example:

Second, the peels were fixed on glass slide bottom Petri dish with a non-toxic silicon gel when all image captured. This gel make sure the peel as flat as possible on slide and give a good view (focus) of field for image capturing.

I hope these information helps.

[CharlotteSai]

I downscaled the resolution to that which is recommend on the job submission page (2880x2048) and exported the sample 6320006-1 to png and it does pick up some stomata:

I don't know for sure how you gathered the images but the samples we use tend to be without the green staining and a little bit more in focus. For Example:

Hi @XDynames, the first image you have shown here is from @thrser or is from us?

[thrser]

Hello, I uploaded this picture, the plant samples were fixed with a certain percentage of ethanol and acetic acid mixture.

[CharlotteSai]

Hello, I uploaded this picture, the plant samples were fixed with a certain percentage of ethanol and acetic acid mixture.

OK, the fixation method itself shouldn't affected the present of image capturing, as I almost thought your image example is from our barley images at the first place, but it looks a little bit blurry. Any chance the image can be more focused to have clearer boundaries of stomatal complex? It doesn't have to be focused for every single stoma, but as much as possible.