BioImageAnalysisNotebooks

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Hey @haesleinhuepf Low priority issue, but when I try to browse the notebooks on a widescreen monitor that is rotated (e.g. tall and narrow), the table of contents panel on...

kephale

Hi @haesleinhuepf , how could I miss this? Have been working with jupyterbook myself a lot lately (but for proprietary commercial work) and love it. I am starting this issue...

VolkerH

Issue on page /12a_image_file_formats/opening_czi_files.html

1

The code shown in the notebook used `czifile`. > we will open a .czi file using the [czifile library](https://pypi.org/project/czifile/). But a later sentence contradicts with the previous statement. > It...

tuhulab

Hello , Thank you for your work. There is always a notebook for what I am looking for! In this notebook : https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/20_image_segmentation/Segmentation_3D.html In the section intensity and background correction...

ClementCaporal

I'm mainly reading the notebooks on my iPad in portrait mode. A couple of weeks ago, the navbar stopped working. When I click on the icon at the top left,...

iimog

Questions on page /29_algorithm_validation/validate-spot-counting.html

1

Hello, Thank you for your work. I have two questions concerning the [29_algorithm_validation/validate-spot-counting](https://github.com/haesleinhuepf/BioImageAnalysisNotebooks/blob/main/docs/29_algorithm_validation/validate-spot-counting.ipynb) ## Maximum or sum projection ? ```python def compute_true_positives(distance_matrix, thresh): dist_mat = cle.push(distance_matrix) count_matrix = dist_mat <...

ClementCaporal

haesleinhuepf

add hardware guide for bioimage analysis

4

brief hardware guide for bioimage analysis

jackyko1991

This message was generated by [git-bob](https://github.com/haesleinhuepf/git-bob) (version: 0.2.3, model: gpt-4o-2024-05-13), an experimental AI-based assistant. It can make mistakes and has [limitations](https://github.com/haesleinhuepf/git-bob?tab=readme-ov-file#limitations). Check its messages carefully. Added two Jupyter notebooks to...

github-actions[bot]

In the folder about tabular data wrangling, it would be nice to demonstrate how to use the polars library in two new .ipynb files. The first introduces basic table handling...

haesleinhuepf