Multiple errors

[CliodhnaKate]

I am running ashlar on multiple images from a fluorescence microscope (ome.tif) which has a 3x3 image configuration in the x,y direction and a range of images in the z direction ranging from 1 to 100 at each x,y position image.

I am accessing ASHLAR via the command line:
ashlar "fileseries|C:\Users\Downloads\folder|pattern=j_right_top_red-000_Cycle00001_Ch1_{series:6}.ome.tif|overlap=0.35|height=0.84|width=0.84"
"fileseries|C:\Users\Downloads\folder|pattern=j_right_red-000_Cycle00001_Ch1_{series:6}.ome.tif|overlap=0.35|height=0.84|width=0.84"
"fileseries|C:\Users\Downloads\folder|pattern=j_right_bottom_red-000_Cycle00001_Ch1_{series:6}.ome.tif|overlap=0.35|height=0.84|width=0.84"
"fileseries|C:\Users\Downloads\folder|pattern=j_left_top_red-000_Cycle00001_Ch1_{series:6}.ome.tif|overlap=0.35|height=0.84|width=0.84"
"fileseries|C:\Users\Downloads\folder|pattern=j_left_bottom_red-000_Cycle00001_Ch1_{series:6}.ome.tif|overlap=0.35|height=0.84|width=0.84"
"fileseries|C:\Users\Downloads\folder|pattern=j_left_red-
000_Cycle00001_Ch1_{series:6}.ome.tif|overlap=0.35|height=0.84|width=0.84"
"fileseries|C:\Users\Downloads\folder|pattern=j_right_top_red-000_Cycle00001_Ch1_{series:6}.ome.tif|overlap=0.35|height=0.84|width=0.84"
"fileseries|C:\Users\Downloads\folder|pattern=j_top_red-000_Cycle00001_Ch1_{series:6}.ome.tif|overlap=0.35|height=0.84|width=0.84"
"fileseries|C:\Users\Downloads\folder|pattern=j_center_red-000_Cycle00001_Ch1_{series:6}.ome.tif|overlap=0.35|height=0.84|width=0.84"
"fileseries|C:\Users\Downloads\folder|pattern=j_center_bottom_red-000_Cycle00001_Ch1_{series:6}.ome.tif|overlap=0.3|height=0.84|width=0.84" \

Please see the attached picture below whcih shows the convention
LT = left_top_red, T = top_red, RT = right_top_red, L = left_red, C = center_red, R = right_red, LB = left_bottom_red, BC = center_bottom_red, RB =right_bottom_red

I have a number of errors in both cycle 0 and cycle 1 and then ashlar finishes running. These errors are:

For Cycle 0:

assembling thumbnail 86/98<tifffile.read_uic_tag> failed reading CreateTime with ValueError: no datetime before year 1 (julianday=0)
<tifffile.read_uic_tag> failed reading LastSavedTime with ValueError: no datetime before year 1 (julianday=0)
<tifffile.read_uic_tag> failed reading CreateTime with ValueError: no datetime before year 1 (julianday=0)
<tifffile.read_uic_tag> failed reading LastSavedTime with ValueError: no datetime before year 1 (julianday=0)

For Cycle 1:
jnius.JavaException: JVM exception occurred: (The filename, directory name, or volume label syntax is incorrect) java.io.FileNotFoundException

[jmuhlich]

Are your z-axis images actually a z-stack? Ashlar does not support 3D images.

You could stitch one z-level, but your filenames for the 9 stage positions will need to be identical except for the numbers 0 through 8 somewhere (fileseries was designed under the assumption that the "series" number corresponds to stage position). For example taking Z=50:

0-000_Cycle00001_Ch1_000050.ome.tif
1-000_Cycle00001_Ch1_000050.ome.tif
2-000_Cycle00001_Ch1_000050.ome.tif
...
8-000_Cycle00001_Ch1_000050.ome.tif

Then your ashlar command line would be:
ashlar "fileseries|C:\Users\Downloads\folder|pattern={series}-000_Cycle00001_Ch1_000050.ome.tif|overlap=0.35|height=3|width=3|pixel_size=0.84"
Note that width and height denote how many tiles wide and tall your tile grid is, not the pixel dimensions. For pixel size, specify pixel_size (I assumed that's what the 0.84 was in your original command, but do correct that if need be).