plant-seg

plant-seg copied to clipboard

Errors with PlantSeg implementation

6

Hi, I am trying to use plantseg gui to perform segmentation of cells in confocal images. I am however, encountering this issue with patch size constantly. The size of the...

upasana99

yaml.scanner.ScannerError: mapping values are not allowed here

1

Hi Plant-Seg, After I installed plantseg via mamba and run it, I get the following error. I tried to change the config file, but I always got the same error....

e-tomato

Plantseg --gui, no buttons to begin the workflow

10

Hi, I just noticed that actually on the latest update, there are no buttons for starting the workflow on the gui (not napari). See image below. 

Giannisbiol

qin-yu

Proofreading tool doesn't allow adding scribbles

1

Hello, While using the proofreading tool, the person helping me with annotation encounters the following problem: Marking with the brush only works half of the time. I am guessing that...

Buglakova

Expected step: 1. Find HDF5 file 2. Load "raw" dataset 3. Load "label" dataset Now: 1. Find HDF5 file 2. Load "raw" dataset 3. Find a random file 4. Find...

qin-yu

`Need more labels` error from `vigra` during watershed in classic GUI

1

We cant afford to downsample the image or crop further the image. Would be great if there are other ways to fix this issue. 

athulrv

Error while trying to open GUI in the latest PlantSeg version

9

Hello, Facing an issue while trying to open the GUI for the latest version of PlantSeg 1.8.1 after an install in a fresh environment `ModuleNotFoundError: No module named 'bioimage.io'` (same...

adkrishnan

Watershed uses only one CPU and runs very slow on large volumes

2

I'm running PlantSeg for FOR2581 but found watershed step uses only one CPU. I'll try to improve it but please stop me if it's not possible @lorenzocerrone

qin-yu

Model resolution should allow `None` to avoid a default like `(1.0, 1.0, 1.0)`

2

A default but wrong resolution might cause problem in situations such as rescaling.

qin-yu