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Hello, nice to meet you. The experiments you made were really great and I want to find the axon tracks in human brain just like your elife paper said. I chose the `GW24` dataset you reconstructed usin…
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Refactor `recOrder ` calibration module such that
* it is independent of LC voltage control device - TriggerScope or NIDaq
* it is independent of image acquisition software - MicroManager, pycromana…
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`recOrder` is used in scientific experiments where keeping track of the large sets of parameters is essential to both reliable analysis and future reference.
Due to the complex nature of these par…
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**Problem**
Currently, we implement following compute in the processing step of the pipeline:
* QLIPP: pixel-wise reconstruction of retardance and deconvolution of phase from brightfield.
* Fluores…
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The time to reconstruct z-stacks is not linear and quickly becomes an issue reconstructing >50 slice z-stacks. These stacks have shapes (5,61,2048,2048) for 5-state polarization, Z,Y, X.
The issue…
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Here's a minimal demonstration of the issue
```
>>> from iohub.reader import imread
>>> reader = imread('/hpc/projects/compmicro/rawdata/other/NIC QLIPP/2022_12_01 PtK cells/FOV1_1')
>>> reader.…
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I was trying to write the array into a newly created position and get an error during write due to size of the`np.array()` which is (1,1,201,2048,2048) `dtype= np.float64`. This error is related to th…
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Related to https://github.com/czbiohub/iohub/issues/82
The `ZarrConverter` cannot handle 3D+2D MM datasets (datasets where one or more of the MDA channels has the "acquire z-stack" box unchecked). …
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The following steps illustrate the problem:
- Set "Illumination Scheme" to "5-State"
- "Run Calibration"
- "Acquire Birefringence"
- Set "Illumination Scheme" to "4-State" (without re-running the …
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Issue: We want to reconstruct phase and denoise the channels simultaneously. Denoising of phase works. However, there is an issue when defining the fluorescence channel as target channel. It does not …