bryanhe / st-net Goto Github PK

I have trouble opening/wget http://www.spatialtranscriptomicsresearch.org/.
It is just me or the server is down?

Dear Bryan He,

Thank you very much for your great model ST-Net.
I would like to use your model with the dataset which you used in your paper.
But, I could not find it in the web site.
https://www.spatialresearch.org/resources-published-datasets/

Is it possible to access those datasets?

Thanks again.

Hello,

I tried to download data but it seems this link (http://www.spatialtranscriptomicsresearch.org) does not work. The browser says the server cannot be found.

Could you please help me out?

Thanks

Hi

I am trying to replicate stnet results on the original data. While running python3 -m stnet prepare spatial the code asks for _coords.tsv file which is not present in the datasets.
Do I need to create it from the metadata or can I download it from some source?

Please help

Thanks

Hi Bryan,

I am trying to run the code. I download the stent folder and put it into /lib/python3.6/site-packages/ . And I also downloaded the whole folder and run the setup.py to set up the environment. I downloaded the data from https://data.mendeley.com/datasets/29ntw7sh4r/2 which is the breast cancer data. I put the stent.cfg file in my test folder and run python3 -m stnet prepare spatial from the test folder but it shows the following error:

FileNotFoundError: [Errno 2] No such file or directory: 'my environment path/lib/python3.6/site-packages/stnet/utils/ensembl.tsv'

My cfg file looks like this:
SPATIAL_RAW_ROOT = "test folder"/input
SPATIAL_PROCESSED_ROOT = "test folder"/input-patch

And the data in the input folder is BC23209_C1_stdata.tsv HE_BC23209_C1.jpg spots_BC23209_C1.csv.

I am new to python so maybe my question is silly. It would be super helpful if you can tell me where I am wrong. Thanks!

Jiawen

Not sure if @bryanhe or anyone here has encountered the same problem as me during the pre-processing stage:

While doing command $python3 -m stnet prepare spatial, there is a DecompressionBombWarning following by TypeError as below:

INFO     [08/29 09:46:19] Loading raw data...
100%|██████████████████████████████████████████████████████████████| 68/68 [00:09<00:00,  8.02it/s]
INFO     [08/29 09:46:29] Loading raw data took 9.390724658966064 seconds.
INFO     [08/29 09:46:29] Finding list of genes: 0.22011828422546387
INFO     [08/29 09:46:29] Processing 1 / 23: BT23508
INFO     [08/29 09:46:29] Processing BT23508 D2...
INFO     [08/29 09:46:30] Adding zeros and ordering columns: 1.4410650730133057
INFO     [08/29 09:46:33] Extracting counts: 3.0241270065307617
INFO     [08/29 09:46:34] Extracting tumors: 0.189774751663208
/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/PIL/Image.py:2735: DecompressionBombWarning: Image size (92491075 pixels) exceeds limit of 89478485 pixels, could be decompression bomb DOS attack.
  DecompressionBombWarning,
INFO     [08/29 09:46:35] Loading image: 1.348219394683838
Traceback (most recent call last):
  File "/home/xx/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4380, in get_value
    return libindex.get_value_box(s, key)
  File "pandas/_libs/index.pyx", line 52, in pandas._libs.index.get_value_box
  File "pandas/_libs/index.pyx", line 48, in pandas._libs.index.get_value_at
  File "pandas/_libs/util.pxd", line 113, in pandas._libs.util.get_value_at
  File "pandas/_libs/util.pxd", line 98, in pandas._libs.util.validate_indexer
TypeError: 'str' object cannot be interpreted as an integer

and during handling of the above exception, another exception for KeyError: 'pixel_x' occurred:

Traceback (most recent call last): File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/home/george/anaconda3/envs/stnet/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/george/ST-Net-master/stnet/__main__.py", line 8, in <module> stnet.main() File "/home/george/ST-Net-master/stnet/main.py", line 15, in main func(args) File "/home/george/ST-Net-master/stnet/cmd/prepare/spatial.py", line 94, in spatial x = int(round(row["pixel_x"])) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/series.py", line 868, in __getitem__ result = self.index.get_value(self, key) File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4388, in get_value raise e1 File "/home/george/anaconda3/envs/stnet/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 4374, in get_value tz=getattr(series.dtype, 'tz', None)) File "pandas/_libs/index.pyx", line 81, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 89, in pandas._libs.index.IndexEngine.get_value File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'pixel_x'

Hello Bryan,

I recently read your work stnet and am very interested in the model. I tried your command "python3 -m stnet prepare spatial" but there is no ensembl.pkl or ensembl.tsv files in the utils folder.

Thanks,
Kenong

Hello everyone!
I have a mysterious problem..
Whenever my colleague performed cross-validation with GUP mode, a beeping noise comes..since this happens only while running cross-validation on GPU mode. It is no issue if he used only the CPU to run this program.

it occurs within 3-5 mins of starting the cross-validation process.
Can somebody help me out here??

This is our workstation configuration:
Processor (AMD RYZEN Threadripper 3rd Gen): 32-Core 3.70 GHz AMD RYZEN Threadripper 3970X 3rd Gen
Air-cooling (CPU)
Memory (DDR4 3200 MHz): 128 GB
GPU Support: 4 GPU-Ready (only for 4x NVIDIA RTX 2080 Ti; 1600W power supply)
Operating System: Ubuntu 20.04
Graphics Card: 2 x NVIDIA RTX A6000 48 GB
NVIDIA NVLink Bridge: 1 x NVLink for 2 x NVIDIA RTX (up to +15% performance)
HDD #1 (Operating System, Applications):1 TB PCI-E 3.0 NVMe SSD
HDD #2:1 TB PCI-E 4.0 NVMe SSD
HDD #3:8 TB HDD
HDD #4:8 TB HDD

Hi @bryanhe ,
I had 2 questions

1. Why did you choose to convert JPEG to TIF tiles, are there any specific reasons why JPG patches should be avoided?
2. What is "histonet" package? , I couldnt find it on PyPI , could you please give the link to the same?

Thank you

Dear Bryan He @bryanhe ,

Thank you very much for your great model ST-Net.
I would like to use your model with the dataset which you used in your paper.
But I get this error , how could we create the pkl , _coords.tsv files etc :

FileNotFoundError: [Errno 2] No such file or directory: '/ST-Net/data/BC24105/BC24105_D1.pkl'

python3 -m stnet prepare spatial

On running this command I have got this error, any idea how should I tackle this...??
File not found, where can I download it from?

Thanking for the help in advance