英文:
Snakemake subtract a mask from two channels
问题
I have a project of several microscopy recordings that I need to process. The recordings have two channels (red and green), so the structure is like this:
rec1/Ch0/video.tif
rec1/Ch1/video.tif
rec2/Ch0/video.tif
rec2/Ch1/video.tif
etc...
I need to do several operations, most of them equally to both channels. For example, cropping, blurring, etc. But then I need to create a mask on the red channel only (Ch0) and apply this mask on both channels to measure the intensity inside the mask. How can I do this?
The result should look like this:
rec1/Ch0/video.tif
rec1/Ch0/video_cropped_blurred.tif
rec1/Ch0/video_cropped_blurred_mask.tif
rec1/Ch0/video_cropped_blurred_mask_measurements.csv
rec1/Ch1/video.tif
rec1/Ch1/video_cropped_blurred.tif
rec1/Ch1/video_cropped_blurred_mask_measurements.csv
rec2/Ch0/video.tif
rec2/Ch0/video_cropped_blurred.tif
rec2/Ch0/video_cropped_blurred_mask.tif
rec2/Ch0/video_cropped_blurred_mask_measurements.csv
rec2/Ch1/video.tif
rec2/Ch1/video_cropped_blurred.tif
rec2/Ch1/video_cropped_blurred_mask_measurements.csv
etc...
So far I have:
import glob
RED_CHANNEL = glob.glob("rec*/Ch0/")
GREEN_CHANNEL = glob.glob("rec*/Ch1/")
rule targets:
input:
red_blur = expand("{red_datasets}video_blurred.tif", red_datasets=RED_CHANNEL),
green_blur = expand("{green_datasets}video_blurred.tif", green_datasets=GREEN_CHANNEL),
red_mask = expand("{red_datasets}video_blurred_mask.tif", red_datasets=RED_CHANNEL),
rule red_blur:
input:
raw_img = "{red_datasets}video.tif"
output:
blurred_img = "{red_datasets}video_blurred.tif"
shell:
"python blur.py -i {input.raw_img} -o {output.blurred_img}"
rule green_blur:
input:
raw_img = "{green_datasets}video.tif"
output:
blurred_img = "{green_datasets}video_blurred.tif"
shell:
"python blur.py -i {input.raw_img} -o {output.blurred_img}"
But I get the following error:
Rules green_blur and red_blur are ambiguous for the file ../Ch0/video.tif
Consider starting rule output with a unique prefix, constrain your wildcards, or use the ruleorder directive.
Wildcards:
green_blur: green_datasets=../Ch0/
red_subtract_background: red_datasets=../Ch0/
Why does the green dataset wildcard also get the Ch0? I could have then only one blur rule, but how would I then create a rule mask that masks Ch1 with the Ch0 mask? How can I access the file rec*/Ch0/video_cropped_blurred_mask.tif
for rules that apply to Ch1?
In other words, how can I make this rule?
rule mask:
input:
img = "{green_datasets}_cropped_blurred.tif",
mask = "{red_datasets}_cropped_blurred_mask.tif"
output:
measurements = "{green_datasets}_mask_measurements.csv"
shell:
"python measure.py -i {input.img} -mask {input.mask} -o {output.measurements}"
Thank you very much!
英文:
I have a project of several microscopy recordings that I need to process. The recordings have two channels (red and green), so the structure is like this:
rec1/Ch0/video.tif
rec1/Ch1/video.tif
rec2/Ch0/video.tif
rec2/Ch1/video.tif
etc..
I need to do several operations, most of them equally to both channels.
For example, cropping, blurring, etc.
But then I need to create a mask on the red channel only (Ch0) and apply this mask on both channels to measure the intensity inside the mask. How can I do this?
The result should look like this:
rec1/Ch0/video.tif
rec1/Ch0/video_cropped_blurred.tif
rec1/Ch0/video_cropped_blurred_mask.tif
rec1/Ch0/video_cropped_blurred_mask_measurements.csv
rec1/Ch1/video.tif
rec1/Ch1/video_cropped_blurred.tif
rec1/Ch1/video_cropped_blurred_mask_measurements.csv
rec2/Ch0/video.tif
rec2/Ch0/video_cropped_blurred.tif
rec2/Ch0/video_cropped_blurred_mask.tif
rec2/Ch0/video_cropped_blurred_mask_measurements.csv
rec2/Ch1/video.tif
rec2/Ch1/video_cropped_blurred.tif
rec2/Ch1/video_cropped_blurred_mask_measurements.csv
etc..
So far I have:
import glob
RED_CHANNEL = glob.glob("rec*/Ch0/")
GREEN_CHANNEL = glob.glob("rec*/Ch1/")
rule targets:
input:
red_blur = expand("{red_datasets}video_blurred.tif", red_datasets=RED_CHANNEL),
green_blur = expand("{green_datasets}video_blurred.tif", green_datasets=GREEN_CHANNEL),
red_mask = expand("{red_datasets}video_blurred_mask.tif", red_datasets=RED_CHANNEL),
rule red_blur:
input:
raw_img ="{red_datasets}video.tif"
output:
blurred_img = "{red_datasets}video_blurred.tif"
shell:
"python blur.py -i {input.raw_img} -o {output.blurred_img}"
rule green_blur:
input:
raw_img ="{green_datasets}video.tif"
output:
blurred_img = "{green_datasets}video_blurred.tif"
shell:
"python blur.py -i {input.raw_img} -o {output.blurred_img}"
But I get the following error:
Rules green_blur and red_blur are ambiguous for the file ../Ch0/video.tif
Consider starting rule output with a unique prefix, constrain your wildcards, or use the ruleorder directive.
Wildcards:
green_blur: green_datasets=../Ch0/
red_subtract_background: red_datasets=../Ch0/
Why does the green dataset wildcard also get the Ch0?
I could have then only one blur rule, but how would I then create a rule mask, that masks Ch1 with the Ch0 mask?
How can I access the file rec*/Ch0/video_cropped_blurred_mask.tif for rules that apply to Ch1?
In other words, how can I make this rule?
rule mask:
input:
img = "{green_datasets}_cropped_blurred.tif",
mask = "{red_datasets}_cropped_blurred_mask.tif"
output:
measurements = "{green_datasets}_mask_measurements.csv"
shell:
"python measure.py -i {input.img} -mask {input.mask} -o {output.measurements}"
Thank you very much!
答案1
得分: 1
翻译后的内容如下:
Echoing @euronion,红色和绿色通配符只是通配符。它们的名称无关紧要,实际上会被替换为.+
正则表达式。但这也赋予了你一些力量,即使用通配符来通用地使用规则。以下是你工作流的重写:
red_channel, green_channel = 0, 1 # 最好在配置中设置
# 获取通道0的记录,当请求所有输出时,将验证通道1是否存在
recordings = glob_wildcards('rec{recording}/Ch0/video.tif').recording
rule targets: # 只需请求最终输出
input:
expand('rec{recording}/Ch{channel}/video_mask_measurements.csv',
recording=recordings,
channels=[red_channel, green_channel],
)
rule blur: # 这可以通用于任何通道
input:
raw_img = "{base}video.tif" # 通配符可以是任何内容
output:
blurred_img = "{base}video_blurred.tif"
shell:
"python blur.py -i {input.raw_img} -o {output.blurred_img}"
rule create_mask:
input:
img = "rec{recording}/Ch{channel}/video_blurred.tif",
output:
mask = "rec{recording}/Ch{channel}/video_mask.tif",
shell:
"python make_mask.py -i {input.img} -o {output}"
rule use_mask: # 这也是通用的
input:
img = "rec{recording}/Ch{channel}/video_blurred.tif",
mask = expand("rec{recording}/Ch{channel}/video_mask.tif",
channel=red_channel, # 但是掩码只能是红色
allow_missing=True),
output:
measurements = "rec{recording}/Ch{channel}/video__mask_measurements.csv"
shell:
"python measure.py -i {input.img} -mask {input.mask} -o {output.measurements}"
blur
、create_mask
和use_mask
适用于任何通道。但是,use_mask
仅请求红色通道的掩码,因此只运行了这个通道。
根据你的文件名,我错过了一个裁剪步骤,但这应该解决了通道的问题。
英文:
Echoing @euronion, the red and green wildcards are just that, wildcards. Their names don't matter and are effectively replaced with a .+
regex. But that also imparts some power that you aren't leveraging, namely using a rule generically using wildcards. Here's a rewrite of your workflow:
red_channel, green_channel = 0, 1 # ideally set in config
# get recordings for ch0, will validate ch1 exists when requesting all outputs
recordings = glob_wildcards('rec{recording}/Ch0/video.tif').recording
rule targets: # need only request final output
input:
expand('rec{recording}/Ch{channel}/video_mask_measurements.csv',
recording=recordings,
channels=[red_channel, green_channel],
)
rule blur: # this can be generic for any channel
input:
raw_img ="{base}video.tif" # wildcard can be anything
output:
blurred_img = "{base}video_blurred.tif"
shell:
"python blur.py -i {input.raw_img} -o {output.blurred_img}"
rule create_mask:
input:
img = "rec{recording}/Ch{channel}/video_blurred.tif",
output:
mask = "rec{recording}/Ch{channel}/video_mask.tif",
shell:
"python make_mask.py -i {input.img} -o {output}"
rule use_mask: # this is also generic
input:
img = "rec{recording}/Ch{channel}/video_blurred.tif",
mask = expand("rec{recording}/Ch{channel}/video_mask.tif",
channel=red_channel, # but the mask can only be red
allow_missing=True),
output:
measurements = "rec{recording}/Ch{channel}/video__mask_measurements.csv"
shell:
"python measure.py -i {input.img} -mask {input.mask} -o {output.measurements}"
blur
, create_mask
, and use_mask
are generic to either channel. However, use_mask
only requests a mask for the red_channel, so that is the only one that is run.
Based on your filenames I missed a cropping step, but this should address the channel issues.
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