Mercurial > repos > goeckslab > mesmer
changeset 2:187918c47051 draft
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mesmer commit 40737a3341bb2352f4f8560889bb53362fd624be
| author | goeckslab |
|---|---|
| date | Wed, 28 Dec 2022 19:26:02 +0000 |
| parents | 02abff468d60 |
| children | c60b810d570d |
| files | Dockerfile macros.xml mesmer.xml test-data/deepcell_test.tiff test-data/test.tiff |
| diffstat | 5 files changed, 198 insertions(+), 44 deletions(-) [+] |
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--- a/Dockerfile Thu Nov 10 20:38:34 2022 +0000 +++ b/Dockerfile Wed Dec 28 19:26:02 2022 +0000 @@ -1,5 +1,7 @@ -ARG VERSION=0.3.1 +ARG VERSION=0.12.3 -FROM vanvalenlab/deepcell-applications:${VERSION} +FROM vanvalenlab/deepcell-tf:${VERSION} + +RUN pip install imagecodecs zarr ENTRYPOINT []
--- a/macros.xml Thu Nov 10 20:38:34 2022 +0000 +++ b/macros.xml Wed Dec 28 19:26:02 2022 +0000 @@ -2,7 +2,7 @@ <macros> <xml name="requirements"> <requirements> - <container type="docker">quay.io/goeckslab/mesmer:@TOOL_VERSION@</container> + <container type="docker">quay.io/goeckslab/deepcell:@TOOL_VERSION@</container> </requirements> </xml> <xml name="stdio"> @@ -25,16 +25,42 @@ description="Out of Memory" /> </stdio> </xml> - <xml name="version_cmd"> - <version_command>@CMD_BEGIN@ --help</version_command> + + <xml name="watershed_adv_options"> + <param name="maxima_smooth" type="integer" value="0" label="Maxima Smooth"/> + <param name="interior_threshold" type="float" value="0.2" label="Interior Threshold"/> + <param name="interior_smooth" type="integer" value="2" label="Interior Smooth"/> + <param name="small_objects_threshold" type="integer" value="15" label="Small Objects Threshold"/> + <param name="fill_holes_threshold" type="integer" value="15" label="Fill Holes Threshold"/> + <param name="radius" type="integer" value="1" label="Radius"/> </xml> + + <xml name="nuclear_options_macro"> + <section name="nuclear_options" title="Nuclear Options" expanded="true"> + <param name="pixel_expansion" type="integer" optional="true" label="Number of pixels to expand nucleus"/> + <param name="maxima_threshold" type="float" value="0.1" label="Maxima Threshold"/> + <section name="adv_options" title="Advanced Nuclear Options" expanded="false"> + <expand macro="watershed_adv_options"/> + </section> + </section> + </xml> + + <xml name="wc_options_macro"> + <section name="wc_options" title="Whole Cell Options" expanded="true"> + <param name="wc_channels" type="text" value="1" label="The numerical indices of the channel(s) for the membrane markers" help="No quotes, separated by comma. e.g. 0, 1."/> + <param name="maxima_threshold" type="float" value="0.075" label="Maxima Threshold"/> + <section name="adv_options" title="Advanced Whole Cell Options" expanded="false"> + <expand macro="watershed_adv_options"/> + </section> + </section> + </xml> + <xml name="citations"> <citations> <citation type="doi">10.1038/s41587-021-01094-0</citation> </citations> </xml> - <token name="@TOOL_VERSION@">0.3.1</token> - <token name="@VERSION_SUFFIX@">1</token> - <token name="@CMD_BEGIN@">python /usr/src/app/run_app.py mesmer</token> + <token name="@TOOL_VERSION@">0.12.3</token> + <token name="@VERSION_SUFFIX@">2</token> </macros>
--- a/mesmer.xml Thu Nov 10 20:38:34 2022 +0000 +++ b/mesmer.xml Wed Dec 28 19:26:02 2022 +0000 @@ -7,63 +7,189 @@ <expand macro="requirements"/> <expand macro="stdio"/> - <expand macro="version_cmd"/> <command detect_errors="exit_code"><![CDATA[ - ln -s '$nuclear_image' 'input.tif' && - @CMD_BEGIN@ - --output-directory ./ - --output-name 'mask.tif' - --nuclear-image 'input.tif' - --nuclear-channel $nuclear_channel - --compartment $compartment - --image-mpp $image_mpp - $squeeze + python $script + ]]></command> + <configfiles> + <configfile name="script"> +import argparse +import os +import sys + +import numpy as np +import tifffile +import zarr + +from deepcell.applications import Mesmer + +level = 0 +is_ome=False +#if $image.file_ext == "ome.tiff": +is_ome=True +#end if + +## Grab params +nuc_kwargs = {} +wc_kwargs = {} + + +with tifffile.TiffFile("$image", is_ome=is_ome) as tiff: + + # Read single pyramid level + level_array = zarr.open(tiff.aszarr(series = 0, level = level)) + + ## grab the nuclear and membrane channels based on their indices add the markers along the channel axis + ## Tifffile should always read as (channel,X,Y) + #if $compartment_select.compartment != 'whole-cell': + nuc_kwargs = { + #if $compartment_select.nuclear_options.pixel_expansion != '': + 'pixel_expansion': $compartment_select.nuclear_options.pixel_expansion, + #end if + #for $key, $value in $dict.items($compartment_select.nuclear_options.adv_options) + '$key': $value, + #end for + 'maxima_threshold': $compartment_select.nuclear_options.maxima_threshold + } + #end if + + nuclear_indices = [int(x) for x in $nuclear_channels.split(',')] + nuclear_channels = level_array.oindex[nuclear_indices, :, :] + nuclear_channels = np.sum(nuclear_channels, axis = 0) - #if $membrane_select.membrane_segment == "True": - --membrane-image '$membrane_select.membrane_image' - --membrane-channel '$membrane_select.membrane_channel' + #if $compartment_select.compartment != 'nuclear': + wc_kwargs = { + #for $key, $value in $dict.items($compartment_select.wc_options.adv_options) + '$key': $value, + #end for + 'maxima_threshold': $compartment_select.wc_options.maxima_threshold + } + + membrane_indices = [int(x) for x in $compartment_select.wc_options.wc_channels.split(',')] + membrane_channels = level_array.oindex[membrane_indices, :, :] + membrane_channels = np.sum(membrane_channels, axis = 0) + #end if + + ## stack the nuclear and membrane composite channels with nuclear in channel 0 and mem in channel 1 + ## mesmer expects dimensions to be (X,Y,Channel) so axis = -1 + #if $compartment_select.compartment == 'nuclear': + membrane_channels = np.zeros(nuclear_channels.shape) #end if - ]]></command> + formatted_image = np.stack((nuclear_channels,membrane_channels), axis=-1) + + ## add batch dimension. Will have to be squeezed out later + formatted_image = np.expand_dims(formatted_image, 0) + +## Create the application +app = Mesmer() + +## Run segmentation +mask = app.predict( + formatted_image, + image_mpp = $image_mpp, + compartment = "$compartment_select.compartment", + pad_mode = 'constant', + postprocess_kwargs_whole_cell = wc_kwargs, + postprocess_kwargs_nuclear = nuc_kwargs) +#if $squeeze: +mask = np.squeeze(mask) +#end if + +#if $compartment_select.compartment == 'both': +## split the two-channel mask into separate outputs + #if $squeeze: +tifffile.imsave( "WC_output_mask.tif", mask[:,:,0]) +tifffile.imsave("NU_output_mask.tif", mask[:,:,1]) + #else: +tifffile.imsave( "WC_output_mask.tif", mask[:,:,:,0]) +tifffile.imsave("NU_output_mask.tif", mask[:,:,:,1]) + #end if +#else: +## save single-channel mask outputs as a tiff +tifffile.imsave("mask.tif", mask) +#end if + </configfile> + </configfiles> <inputs> - <param name="nuclear_image" type="data" format="tiff, ome.tiff" label="Image containing the nuclear marker(s)"/> - <param name="nuclear_channel" type="integer" value="0" label="The numerical index of the channel(s) from nuclear-image"/> - <param name="compartment" type="select" label="Compartment for segmentation prediction: "> - <option selected="true" value="whole-cell">Whole cell</option> - <option value="nuclear">Nuclear</option> - </param> + <param name="image" type="data" format="tiff, ome.tiff" label="Image containing the all marker(s)"/> + <param name="nuclear_channels" type="text" value="0" label="The numerical indices of the channel(s) for the nuclear markers" help="No quotes, separated by comma. e.g. 0, 1."/> <param name="image_mpp" type="float" value="0.5" label="Resolution of the image in microns-per-pixel"/> - <param name="squeeze" type="boolean" truevalue="--squeeze" falsevalue="" checked="false" label="Whether to np.squeeze the outputs before saving"/> - <conditional name="membrane_select"> - <param name="membrane_segment" type="select" label="Segment with Cell Membrane"> - <option selected="True" value="False">No</option> - <option value="True">Yes</option> + <param name="squeeze" type="boolean" checked="true" label="Whether to np.squeeze the outputs before saving"/> + <conditional name="compartment_select"> + <param name="compartment" type="select" label="Compartment for segmentation prediction: "> + <option selected="true" value="whole-cell">Whole cell</option> + <option value="nuclear">Nuclear</option> + <option value="both">Both</option> </param> - <when value="True"> - <param name="membrane_image" type="data" format="tiff, ome.tiff" label="The path to an image containing the membrane marker(s)"/> - <param name="membrane_channel" type="integer" value="0" label="The numerical index of the channel(s) from membrane-image"/> + <when value="nuclear"> + <expand macro="nuclear_options_macro"/> </when> - <when value="False" /> + <when value="whole-cell"> + <expand macro="wc_options_macro"/> + </when> + <when value="both"> + <expand macro="nuclear_options_macro"/> + <expand macro="wc_options_macro"/> + </when> </conditional> </inputs> + <outputs> - <data format="tiff" name="mask" from_work_dir="mask.tif" label="${tool.name} on ${on_string}: Mask"/> + <data format="tiff" name="nu_mask" from_work_dir="NU_output_mask.tif" label="${tool.name} on ${on_string}: Nuclear Mask"> + <filter>compartment_select['compartment'] == 'both'</filter> + </data> + <data format="tiff" name="wc_mask" from_work_dir="WC_output_mask.tif" label="${tool.name} on ${on_string}: Whole Cell Mask"> + <filter>compartment_select['compartment'] == 'both'</filter> + </data> + <data format="tiff" name="mask" from_work_dir="mask.tif" label="${tool.name} on ${on_string}: Mask"> + <filter>compartment_select['compartment'] != 'both'</filter> + </data> </outputs> <tests> - <test> - <param name="nuclear_image" value="test.tiff" /> + <test> + <param name="image" value="deepcell_test.tiff" ftype="tiff"/> <param name="compartment" value="nuclear" /> - <param name="membrane_segment" value="False" /> <param name="image_mpp" value="0.65" /> - <param name="squeeze" value="--squeeze" /> + <param name="squeeze" value="True" /> <output name="mask" ftype="tiff"> <assert_contents> - <has_size value="360000" delta="1000" /> + <has_size value="1049000" delta="1000" /> </assert_contents> </output> </test> - </tests> + <test> + <param name="image" value="deepcell_test.tiff" ftype="tiff"/> + <param name="compartment" value="whole-cell" /> + <param name="wc_channels" value="0, 1" /> + <param name="maxima_threshold" value="0.075" /> + <param name="image_mpp" value="0.65" /> + <param name="squeeze" value="True" /> + <output name="mask" ftype="tiff"> + <assert_contents> + <has_size value="1049000" delta="1000" /> + </assert_contents> + </output> + </test> + <test> + <param name="image" value="deepcell_test.tiff" ftype="tiff"/> + <param name="compartment" value="both" /> + <param name="image_mpp" value="0.65" /> + <param name="wc_channels" value="1" /> + <param name="nuclear_channels" value="0" /> + <param name="squeeze" value="True" /> + <output name="wc_mask" ftype="tiff"> + <assert_contents> + <has_size value="1049000" delta="1000" /> + </assert_contents> + </output> + <output name="nu_mask" ftype="tiff"> + <assert_contents> + <has_size value="1049000" delta="1000" /> + </assert_contents> + </output> + </test> + </tests> <help><![CDATA[ ------ Mesmer