Commit 5e973eb 1 parent ebb2c28 commit 5e973eb Copy full SHA for 5e973eb
File tree 1 file changed +7
-7
lines changed
1 file changed +7
-7
lines changed Original file line number Diff line number Diff line change 1
1
steps:
2
- - bbbcdownload:
2
+ bbbcdownload:
3
3
in:
4
4
name: !ii BBBC001
5
5
outDir: !ii bbbcdownload.outDir
6
6
out:
7
7
- outDir: !& bbbcdownload.outDir
8
- - subdirectory:
8
+ subdirectory:
9
9
in:
10
10
directory: !* bbbcdownload.outDir
11
11
glob_pattern: !ii bbbcdownload.outDir/BBBC/BBBC001/raw/Images/human_ht29_colon_cancer_1_images/
12
12
out:
13
13
- subdirectory: !& subdirectory.subdirectory
14
- - file-renaming:
14
+ file-renaming:
15
15
in:
16
16
filePattern: !ii .*_{row:c}{col:dd}f{f:dd}d{channel:d}.tif
17
17
inpDir: !* subdirectory.subdirectory
18
18
outDir: !ii file-renaming.outDir
19
19
outFilePattern: !ii x{row:dd}_y{col:dd}_p{f:dd}_c{channel:d}.tif
20
20
out:
21
21
- outDir: !& file-renaming.outDir
22
- - ome-converter:
22
+ ome-converter:
23
23
in:
24
24
fileExtension: !ii .ome.tif
25
25
filePattern: !ii .*.tif
26
26
inpDir: !* file-renaming.outDir
27
27
outDir: !ii omeconverter.outDir
28
28
out:
29
29
- outDir: !& omeconverter.outDir
30
- - montage:
30
+ montage:
31
31
in:
32
32
filePattern: !ii x00_y03_p{p:dd}_c0.ome.tif
33
33
inpDir: !* omeconverter.outDir
34
34
layout: !ii p
35
35
outDir: !ii montage.outDir
36
36
out:
37
37
- outDir: !& montage.outDir
38
- - image_assembler:
38
+ image_assembler:
39
39
in:
40
40
imgPath: !* omeconverter.outDir
41
41
outDir: !ii image_assembler.outDir
42
42
stitchPath: !* montage.outDir
43
43
out:
44
44
- outDir: !& image_assembler.outDir
45
- - precompute_slide:
45
+ precompute_slide:
46
46
in:
47
47
imageType: !ii image
48
48
inpDir: !* image_assembler.outDir
You can’t perform that action at this time.
0 commit comments