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documents:140326jointcourse
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documents:140326jointcourse [2016/05/24 05:46] 127.0.0.1 external edit |
documents:140326jointcourse [2017/06/06 20:08] (current) kota github username changed |
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| https://bio-it.embl.de/joint-training | https://bio-it.embl.de/joint-training | ||
| - | https://github.com/cmci/HTManalysisCourse/blob/master/CentreCourseProtocol.md | + | https://github.com/miura/HTManalysisCourse/blob/master/CentreCourseProtocol.md |
| <markdown> | <markdown> | ||
| Line 502: | Line 502: | ||
| :check Display Results, Clear results, Exclude on Edges, Include Holes | :check Display Results, Clear results, Exclude on Edges, Include Holes | ||
| - | q1, q3, offset calculation: Copy and paste <https://gist.github.com/cmci/9641262> | + | q1, q3, offset calculation: Copy and paste <https://gist.github.com/miura/9641262> |
| Example results: 2926.0 3854.0 1392.0 | Example results: 2926.0 3854.0 1392.0 | ||
| Line 641: | Line 641: | ||
| Codes used in this interactive session assembled in a file and in | Codes used in this interactive session assembled in a file and in | ||
| - | <https://gist.github.com/cmci/9687511> | + | <https://gist.github.com/miura/9687511> |
| ### File access | ### File access | ||
| Line 1127: | Line 1127: | ||
| A script for processing single image dataset is: | A script for processing single image dataset is: | ||
| - | <https://gist.github.com/cmci/9765308> | + | <https://gist.github.com/miura/9765308> |
| ```python | ```python | ||
| Line 1267: | Line 1267: | ||
| ``` | ``` | ||
| - | <https://gist.github.com/cmci/9644827> | + | <https://gist.github.com/miura/9644827> |
| Line 1389: | Line 1389: | ||
| We will not go over the details of full processing, but the pre-screening code is a good example of accessing multiple files and process images. | We will not go over the details of full processing, but the pre-screening code is a good example of accessing multiple files and process images. | ||
| - | <https://gist.github.com/cmci/9684453> | + | <https://gist.github.com/miura/9684453> |
| Pre-screen results are saved under | Pre-screen results are saved under | ||
| Line 1399: | Line 1399: | ||
| Assembling all the fragments as a single script, here is the final code to submit. | Assembling all the fragments as a single script, here is the final code to submit. | ||
| - | <https://github.com/cmci/HTManalysisCourse/blob/master/measTransportBatch3.py> | + | <https://github.com/miura/HTManalysisCourse/blob/master/measTransportBatch3.py> |
| An important command that appears only here is 'sys.argv`, which holds the argument added in the command line. Try the following to see what is happening. | An important command that appears only here is 'sys.argv`, which holds the argument added in the command line. Try the following to see what is happening. | ||
| Line 1439: | Line 1439: | ||
| Here is the code written by Clemens. | Here is the code written by Clemens. | ||
| - | <https://github.com/cmci/HTManalysisCourse/blob/master/fiji_script.sh> | + | <https://github.com/miura/HTManalysisCourse/blob/master/fiji_script.sh> |
| ```sh | ```sh | ||
documents/140326jointcourse.txt ยท Last modified: 2017/06/06 20:08 by kota
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