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Bug 206 - batch conversion from LSM to TIF does not work in Multi Image Processor
batch conversion from LSM to TIF does not work in Multi Image Processor
Status: RESOLVED WONTFIX
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: Johannes Schindelin
Depends on:
Blocks:
 
Reported: 2010-08-05 13:02 CDT by Jakob Schweizer
Modified: 2012-04-20 23:33 CDT
1 user (show)

See Also:

Description Jakob Schweizer 2010-08-05 13:02:29 CDT
I tried to convert ZEISS LSM stacks into tif-files using Multi Image Processor. It produces a log file (see below) put converts no images.

jakob

Log file:


Converting to Tiff
dir1: Y:\work\image processing\selected rectangles 20100804
dir2: Y:\work\image processing\selected rectangels 20100804 tiff\
1: #351-gold3-gaps-day2-c-0080-0500-min-01.lsm
2: #351-gold3-gaps-day2-a-0032-1250-min-01.lsm
3: #351-gold3-gaps-day2-b-0050-0800-min-02-1hlater.lsm
4: #351-gold3-gaps-day2-c-0200-0200-min-01.lsm
5: #351-gold3-gaps-day2-b-0125-0320-min-01.lsm
6: #351-gold3-gaps-day2-c-1250-0032-min-01.lsm
7: #351-gold3-gaps-day2-a-0050-0800-min-01.lsm
8: #351-gold3-gaps-day2-c-1000-0040-min-01.lsm
9: #351-gold3-gaps-day2-c-0040-1000-min-01.lsm
10: #351-gold3-gaps-day2-c-0160-0250-min-01.lsm
11: #351-gold3-gaps-day2-c-0320-0125-min-01.lsm
12: #351-gold3-gaps-day2-c-0250-0160-min-01.lsm
13: #351-gold3-gaps-day2-c-0400-0100-min-01.lsm
14: #351-gold3-gaps-day2-a-0500-0080-min-01.lsm
15: #351-gold3-gaps-day2-a-0100-0100-min-01.lsm
16: #351-gold3-gaps-day2-b-0080-0500-min-01.lsm
17: #351-gold3-gaps-day2-b-1250-0032-min-01.lsm
18: #351-gold3-gaps-day2-c-0125-0320-min-01.lsm
19: #351-gold3-gaps-day2-b-0200-0200-min-01.lsm
20: #351-gold3-gaps-day2-a-0800-0050-min-01.lsm
21: #351-gold3-gaps-day2-b-1000-0040-min-01.lsm
22: #351-gold3-gaps-day2-b-0400-0100-min-01.lsm
23: #351-gold3-gaps-day2-b-0250-0160-min-01.lsm
24: #351-gold3-gaps-day2-a-0100-0400-min-01.lsm
25: #351-gold3-gaps-day2-b-0320-0125-min-01.lsm
26: #351-gold3-gaps-day2-b-0040-1000-min-01.lsm
27: #351-gold3-gaps-day2-b-0080-0500-min-02-1hlater.lsm
28: #351-gold3-gaps-day2-b-0160-0250-min-01.lsm
29: #351-gold3-gaps-day2-a-1250-0032-min-01.lsm
30: #351-gold3-gaps-day2-b-0800-0050-min-01.lsm
31: #351-gold3-gaps-day2-c-0032-1250-min-01.lsm
32: #351-gold3-gaps-day2-b-0500-0080-min-01.lsm
33: #351-gold3-gaps-day2-a-0080-0500-min-01.lsm
34: #351-gold3-gaps-day2-b-0100-0400-min-01.lsm
35: #351-gold3-gaps-day2-a-0250-0160-min-01.lsm
36: #351-gold3-gaps-day2-a-0400-0100-min-01.lsm
37: #351-gold3-gaps-day2-a-0160-0250-min-01.lsm
38: #351-gold3-gaps-day2-a-0100-0100-min-02.lsm
39: #351-gold3-gaps-day2-a-0040-1000-min-01.lsm
40: #351-gold3-gaps-day2-a-0320-0125-min-01.lsm
41: #351-gold3-gaps-day2-a-200-200-min-01.lsm
42: #351-gold3-gaps-day2-a-1000-0040-min-01.lsm
43: #351-gold3-gaps-day2-c-0050-0800-min-01.lsm
44: #351-gold3-gaps-day2-c-0800-0050-min-01.lsm
45: #351-gold3-gaps-day2-a-0125-0320-min-01.lsm
46: #351-gold3-gaps-day2-c-0500-0080-min-01.lsm
47: #351-gold3-gaps-day2-b-0032-1250-min-01.lsm
48: #351-gold3-gaps-day2-c-0100-0400-min-01.lsm


Information about your version of Java - this information is useful for the Fiji developers:
  os.arch => x86
  os.name => Windows XP
  os.version => 5.1
  java.version => 1.6.0_03
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_03-b05
  java.vm.name => Java HotSpot(TM) Client VM
  java.vm.version => 1.6.0_03-b05
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \
Comment 1 Johannes Schindelin 2012-04-20 23:33:28 CDT
The Multi Image Processor as well as ImageJ1's Batch processor are ill-suited to such a task. It is better to follow this tutorial:

http://fiji.sc/How_to_apply_a_common_operation_to_a_complete_directory