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All of the current analysis steps (`deskew`, `estimate-deskew`, `estimate-bleaching`) read the raw `.ndtiff` as input...a pragmatic choice for our initial analysis steps.
We're now reaching a point…
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The CLI calls should have a standard signature, for example
```sh
mantis COMMAND INPUT_PATH OUTPUT_PATH CONFIG_PATH [OPTIONS]
```
or
```sh
mantis COMMAND -i INPUT_PATH -o OUTPUT_PATH --c…
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I first noticed this issue during a `recOrder` session when I tried to drag and drop a zarr store saved by a recOrder acquisition into napari. The layers and shape populated correctly, but the actual …
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I'm running into issues opening some, but not all, recently acquired ndtiff datasets.
Reproduce with:
```
python
>>> from iohub import read_micromanager
>>> reader = read_micromanager('/hpc/pr…
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Example for this config:
mlflow config: https://mlflow.a100.int.allencell.org/#/experiments/158/runs/c2ad5fd8f7034bb3ac6b874140401c67
save_dir according to mlflow: /allen/aics/assay-dev/users…
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Hi all @jpfeuffer @timosachsenberg @enriquea @dai:
We have recently generated data for almost 100 datasets, differentially expression analyses (DE), and absolute/baseline expression analyses (AE). …
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- Load workflows from github.com/OpenMS/Tutorials folder Workflows
- Add short descriptions and metadata to the workflows after opening them (see the README.MD in the Workflows folder)
- This descri…
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**Describe the bug**
A clear and concise description of what the bug is.
ERROR: Version mismatch: file ./docker-compose.yml specifies version 3.3 but extension file ./docker-compose.labelfree.yml …
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Hi!
I get the following header
```
...
```
when I run with "-f2"
Should it maybe be
```
...
```
or similar?
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Here I present a list of techniques, which I think should be covered by our proteomics tutorials. The list will be incomplete and so far not ordered after priorities. Any help and comments are appreci…