EuBI-Bridge Conversion Examples

Command examples loosely organized by use case. Copy and paste these commands, adjusting input/output paths for your data.

Select your operating system below to see the correct syntax for your platform.

Configuration Management

Reset to Installation Defaults

Unix/macOS & Windows (same for both):

eubi reset_config
eubi show_config

Modify Conversion Settings

Unix/macOS & Windows (same for both):

eubi configure_conversion --channel_intensity_limits from_array
eubi show_config

Display Current Configuration

Unix/macOS & Windows (same for both):

eubi show_config

Basic Unary Conversion

Simple Conversion: Single Input → Single Output

Unix/macOS:

eubi to_zarr small_dataset $HOME/codash_output/small_dataset_zarr

Windows (Command Prompt or PowerShell):

eubi to_zarr small_dataset %USERPROFILE%\codash_output\small_dataset_zarr

Verify the output:

Unix/macOS:

eubi show_pixel_meta $HOME/codash_output/small_dataset_zarr

Windows:

eubi show_pixel_meta %USERPROFILE%\codash_output\small_dataset_zarr

Custom Chunk Sizes

Unix/macOS:

eubi to_zarr small_dataset $HOME/codash_output/small_dataset_zarr_new_chunks --auto_chunk False --y_chunk 64 --x_chunk 64

Windows:

eubi to_zarr small_dataset %USERPROFILE%\codash_output\small_dataset_zarr_new_chunks --auto_chunk False --y_chunk 64 --x_chunk 64

Multiple Resolution Layers (Pyramid)

Unix/macOS:

eubi to_zarr small_dataset $HOME/codash_output/small_dataset_zarr_6_layers --n_layers 6

Windows:

eubi to_zarr small_dataset %USERPROFILE%\codash_output\small_dataset_zarr_6_layers --n_layers 6

Specify the Compression Algorithm

Unix/macOS:

eubi to_zarr small_dataset $HOME/codash_output/small_dataset_zarr_zstd --compressor zstd --compressor_params {level:13}

Windows:

eubi to_zarr small_dataset %USERPROFILE%\codash_output\small_dataset_zarr_6_layers --compressor zstd --compressor_params {level:13}

NGFF v0.5 with Sharding

Unix/macOS:

eubi to_zarr small_dataset $HOME/codash_output/small_dataset_zarr_v0.5 --auto_chunk False --y_chunk 64 --x_chunk 64 --zarr_format 3 --y_shard_coef 5 --x_shard_coef 5

Windows:

eubi to_zarr small_dataset %USERPROFILE%\codash_output\small_dataset_zarr_v0.5 --auto_chunk False --y_chunk 64 --x_chunk 64 --zarr_format 3 --y_shard_coef 5 --x_shard_coef 5

Filtering & Pattern Matching

Include Only TIFF Files

Unix/macOS:

eubi to_zarr small_dataset $HOME/codash_output/small_dataset_zarr_inc_filtered --includes .tiff

Windows:

eubi to_zarr small_dataset %USERPROFILE%\codash_output\small_dataset_zarr_inc_filtered --includes .tiff

Exclude JPG Files

Unix/macOS:

eubi to_zarr small_dataset $HOME/codash_output/small_dataset_zarr_ex_filtered --excludes .jpg

Windows:

eubi to_zarr small_dataset %USERPROFILE%\codash_output\small_dataset_zarr_ex_filtered --excludes .jpg

Include Multiple Formats

Unix/macOS:

eubi to_zarr small_dataset $HOME/codash_output/small_dataset_zarr_multi_inc_filtered --includes .oir,.lsm

Windows:

eubi to_zarr small_dataset %USERPROFILE%\codash_output\small_dataset_zarr_multi_inc_filtered --includes .oir,.lsm

Exclude Multiple Formats

Unix/macOS:

eubi to_zarr small_dataset $HOME/codash_output/small_dataset_zarr_multi_ex_filtered --excludes .oir,.lsm

Windows:

eubi to_zarr small_dataset %USERPROFILE%\codash_output\small_dataset_zarr_multi_ex_filtered --excludes .oir,.lsm

Glob Pattern Matching

Unix/macOS:

eubi to_zarr "small_dataset/*.tif" $HOME/codash_output/small_dataset_zarr_wildcards

Windows:

eubi to_zarr "small_dataset\*.tif" %USERPROFILE%\codash_output\small_dataset_zarr_wildcards

Metadata Inspection & Override

Inspect Source Metadata

Unix/macOS:

eubi show_pixel_meta "small_dataset/*oir"

Windows:

eubi show_pixel_meta "small_dataset\*oir"

Convert with Pixel Scale & Units

Unix/macOS:

eubi to_zarr small_dataset/23052022_D3_0001.oir $HOME/codash_output/small_image_with_metadata --y_scale 0.5 --y_unit micrometer --x_scale 0.5 --x_unit micrometer --channel_labels "0,GFP;1,mCherry;2,BF" --channel_colors "0,yellow;1,magenta;2,white"

Windows:

eubi to_zarr small_dataset\23052022_D3_0001.oir %USERPROFILE%\codash_output\small_image_with_metadata --y_scale 0.5 --y_unit micrometer --x_scale 0.5 --x_unit micrometer --channel_labels "0,GFP;1,mCherry;2,BF" --channel_colors "0,yellow;1,magenta;2,white"

Verify Overridden Metadata

Unix/macOS:

eubi show_pixel_meta "$HOME/codash_output/small_image_with_metadata/*.zarr"

Windows:

eubi show_pixel_meta "%USERPROFILE%\codash_output\small_image_with_metadata\*.zarr"

Update Metadata In Place

Unix/macOS:

eubi update_pixel_meta "$HOME/codash_output/small_image_with_metadata/*.zarr" --y_scale 0.2 --x_scale 0.2

Windows:

eubi update_pixel_meta "%USERPROFILE%\codash_output\small_image_with_metadata\*.zarr" --y_scale 0.2 --x_scale 0.2

Verify Updated Metadata

Unix/macOS:

eubi show_pixel_meta "$HOME/codash_output/small_image_with_metadata/*.zarr"

Windows:

eubi show_pixel_meta "%USERPROFILE%\codash_output\small_image_with_metadata\*.zarr"

Aggregative Conversion

Concatenate multiple input files into a single output file along specified dimensions.

Concatenate Along All Specified Axes

Combine files into channels and time points:

Unix/macOS:

eubi to_zarr multidim_dataset $HOME/codash_output/multidim_dataset_concat_zarr --channel_tag growing,moving,noise --time_tag step --concatenation_axes ct

Windows:

eubi to_zarr multidim_dataset %USERPROFILE%\codash_output\multidim_dataset_concat_zarr --channel_tag growing,moving,noise --time_tag step --concatenation_axes ct

With Nested Directory Structure

Unix/macOS:

eubi to_zarr multidim_dataset_nested $HOME/codash_output/multidim_dataset_nested_concat_zarr --channel_tag growing,moving,noise --time_tag step --concatenation_axes ct

Windows:

eubi to_zarr multidim_dataset_nested %USERPROFILE%\codash_output\multidim_dataset_nested_concat_zarr --channel_tag growing,moving,noise --time_tag step --concatenation_axes ct

Specify Channel Order

Unix/macOS:

eubi to_zarr multidim_dataset_nested $HOME/codash_output/multidim_dataset_nested_concat_zarr --channel_tag noise,growing,moving --time_tag step --concatenation_axes ct --override_channel_names

Windows:

eubi to_zarr multidim_dataset_nested %USERPROFILE%\codash_output\multidim_dataset_nested_concat_zarr --channel_tag noise,growing,moving --time_tag step --concatenation_axes ct --override_channel_names

Advanced Aggregation

Concatenate Along Time Only

Unix/macOS:

eubi to_zarr multidim_dataset $HOME/codash_output/multidim_dataset_concat_along_time_zarr --channel_tag moving,noise,growing --time_tag step --concatenation_axes t --override_channel_names

Windows:

eubi to_zarr multidim_dataset %USERPROFILE%\codash_output\multidim_dataset_concat_along_time_zarr --channel_tag moving,noise,growing --time_tag step --concatenation_axes t --override_channel_names

Aggregation with Pattern Filter

Unix/macOS:

eubi to_zarr "medium_dataset/PK2*.ome.tiff" $HOME/codash_output/multidim_dataset_concat_filtered_zarr --channel_tag ch --concatenation_axes c --skip_dask

Windows:

eubi to_zarr "medium_dataset\PK2*.ome.tiff" %USERPROFILE%\codash_output\multidim_dataset_concat_filtered_zarr --channel_tag ch --concatenation_axes c --skip_dask

Aggregation with Full Metadata Override

Unix/macOS:

eubi to_zarr multidim_dataset $HOME/codash_output/multidim_dataset_concat_zarr_with_metadata --channel_tag moving,noise,growing --time_tag step --concatenation_axes ct --time_scale 18 --time_unit millisecond --y_scale 0.5 --y_unit micrometer --x_scale 0.5 --x_unit micrometer --override_channel_names --channel_colors "0,red;1,green;2,white"

Windows:

eubi to_zarr multidim_dataset %USERPROFILE%\codash_output\multidim_dataset_concat_zarr_with_metadata --channel_tag moving,noise,growing --time_tag step --concatenation_axes ct --time_scale 18 --time_unit millisecond --y_scale 0.5 --y_unit micrometer --x_scale 0.5 --x_unit micrometer --override_channel_names --channel_colors "0,red;1,green;2,white"

Aggregation with Time Range Limit

Unix/macOS:

eubi to_zarr multidim_dataset $HOME/codash_output/multidim_dataset_concat_zarr_with_metadata --channel_tag moving,noise,growing --time_tag step --concatenation_axes ct --time_scale 18 --time_unit millisecond --y_scale 0.5 --y_unit micrometer --x_scale 0.5 --x_unit micrometer --override_channel_names --channel_colors "0,red;1,green;2,white" --time_range 0,5

Windows:

eubi to_zarr multidim_dataset %USERPROFILE%\codash_output\multidim_dataset_concat_zarr_with_metadata --channel_tag moving,noise,growing --time_tag step --concatenation_axes ct --time_scale 18 --time_unit millisecond --y_scale 0.5 --y_unit micrometer --x_scale 0.5 --x_unit micrometer --override_channel_names --channel_colors "0,red;1,green;2,white" --time_range 0,5

Multi-Series Datasets

Convert Selected Series Only

Unix/macOS:

eubi to_zarr medium_dataset/19_07_19_Lennard.lif $HOME/codash_output/multiseries_dataset --scene_index 2,4,6

Windows:

eubi to_zarr medium_dataset\19_07_19_Lennard.lif %USERPROFILE%\codash_output\multiseries_dataset --scene_index 2,4,6

Convert All Series from CZI Files

Unix/macOS:

eubi to_zarr "medium_dataset/*.czi" $HOME/codash_output/multiseries_dataset --scene_index all

Windows:

eubi to_zarr "medium_dataset\*.czi" %USERPROFILE%\codash_output\multiseries_dataset --scene_index all

CSV Based Processing

Create a CSV File

Find or create selection.csv. Its content should be similar to:

input_path,output_path,y_scale,x_scale,y_unit,x_unit,channel_labels
small_dataset/image1.tif,output/image1_zarr,0.5,0.5,micrometer,micrometer,"0,Red;1,Green"
small_dataset/image2.czi,output/image2_zarr,1.0,1.0,micrometer,micrometer,"0,DAPI;1,GFP"

Convert All Files in CSV

Unix/macOS & Windows:

eubi to_zarr selection.csv $HOME/codash_output/from_csv_zarr

Windows:

eubi to_zarr selection.csv %USERPROFILE%\codash_output\from_csv_zarr

Verify Results

Unix/macOS:

eubi show_pixel_meta $HOME/codash_output/from_csv_zarr

Windows:

eubi show_pixel_meta %USERPROFILE%\codash_output\from_csv_zarr

Zarr-to-Zarr Conversion

Re-chunk and reformat existing OME-Zarr files:

Unix/macOS:

eubi to_zarr $HOME/codash_output/multidim_dataset_concat_filtered_zarr/PK2_ATH_5to20_20240705_MID_01_ch_cset.ome.zarr $HOME/codash_output/multidim_dataset_concat_filtered_zarr_newchunks_newshards_v0.5 --auto_chunk False --zarr_format 3 --y_shard_coef 5 --x_shard_coef 5

Windows:

eubi to_zarr %USERPROFILE%\codash_output\multidim_dataset_concat_filtered_zarr\PK2_ATH_5to20_20240705_MID_01_ch_cset.ome.zarr %USERPROFILE%\codash_output\multidim_dataset_concat_filtered_zarr_newchunks_newshards_v0.5 --auto_chunk False --zarr_format 3 --y_shard_coef 5 --x_shard_coef 5

EuBI-Bridge Conversion Examples

Table of Contents

Configuration Management

Reset to Installation Defaults

Modify Conversion Settings

Display Current Configuration

Basic Unary Conversion

Simple Conversion: Single Input → Single Output

Custom Chunk Sizes

Multiple Resolution Layers (Pyramid)

Specify the Compression Algorithm

NGFF v0.5 with Sharding

Filtering & Pattern Matching

Include Only TIFF Files

Exclude JPG Files

Include Multiple Formats

Exclude Multiple Formats

Glob Pattern Matching

Metadata Inspection & Override

Inspect Source Metadata

Convert with Pixel Scale & Units

Verify Overridden Metadata

Update Metadata In Place

Verify Updated Metadata

Aggregative Conversion

Concatenate Along All Specified Axes

With Nested Directory Structure

Specify Channel Order

Advanced Aggregation

Concatenate Along Time Only

Aggregation with Pattern Filter

Aggregation with Full Metadata Override

Aggregation with Time Range Limit

Multi-Series Datasets

Convert Selected Series Only

Convert All Series from CZI Files

CSV Based Processing

Create a CSV File

Convert All Files in CSV

Verify Results

Zarr-to-Zarr Conversion