Commit 27cf0858 authored by r03ert0's avatar r03ert0

Merge branch 'master' into fix-nii-headers-for-masks

parents 472cb2db 1a669c38
Come to our [**dolphin brain**](http://brainbox.pasteur.fr/mri?url=http://braincatalogue.org/data/Bottlenose_dolphin/MRI-n4.nii.gz) , (log in with your GitHub account) and select the Cerebrum from the Braincatalogue project and **join our segmentation sprint!**
<img width="769" alt="screen shot 2017-06-01 at 11 08 34" src="https://cloud.githubusercontent.com/assets/6297454/26672835/f7892d80-46ba-11e7-8be8-51adbee9288d.png">
When you have done 1 slice,
* add your name or github handle to our BRAINMAPPERS.md file
* add the slice number where you have been working (currently, 111 & 112 are done, you could continue with 113++)
* add "length:..." and
* "volume:..." from the upper left corner of the BrainBox viewer into the file (just for the fun!! :D)
* and make a pull request!
The best devices for drawing over the brain are tablets with pens. With a computer mouse or trackpad it is a bit more tedious but works very fine as well 😃 Looking forward to seeing you!
Just say hi in the BrainBox chat and we will guide you to the view where we are currently working.
We will work in an axial slice (113++) and erase all the parts of the mask that cover the sulci of the brain. You see the impressively folded structure of the dolphin brain. The sulci, which are the valleys of the folds, appear darker. We erase them from the mask to being able to reconstruct the 3D surface preserving the folding.
**It's fun! Join us! :)** Careful! It's addictive! <3 😄
![gyrus_sulcus](https://cloud.githubusercontent.com/assets/6297454/26672808/de7c347c-46ba-11e7-9f19-01fef1da9295.png)
We are the brain mappers! /
Here, we are segmenting an amazingly folded [**dolphin brain**](http://brainbox.pasteur.fr/mri?url=http://braincatalogue.org/data/Bottlenose_dolphin/MRI-n4.nii.gz). Once you clicked the link, you will find our work in 'Cerebrum' annotation layer from the Braincatalogue project. You can **join our segmentation sprint any time!** You can also choose a different species to work on, if you prefer! Any contributions are featured below.
<img width="769" alt="screen shot 2017-06-01 at 11 08 34" src="https://cloud.githubusercontent.com/assets/6297454/26672835/f7892d80-46ba-11e7-8be8-51adbee9288d.png">
**Our BrainMapper team**
current Volume segmented: **509 491 mm3** (please update! :D)
Name: ** **
GitHub:
Species:
Slice numbers:
Length: mm
Volume: mm3
Name: **katja**
GitHub: katjaq
Species: Bottlenose dolphin
Slice numbers: axial 112
Length: mm
Volume: 509491 mm3
<!-- Thank you so much for your contribution to BrainBox! <3 -->
<!-- Please find a short title for your pull request and describe your changes on the following line: -->
---
<!-- Please go through our check list and check the functionalities which might be affected by your code changes. Replace each `[ ]` by `[X]` when the step is complete.-->
- [ ] These changes fix #__ (github issue number if applicable).
- [ ] All BrainBox tools behave as expected:
* **KEYS**
* right and left arrow keys
- [ ] jump to next or previous slice within one brain, respectively
- [ ] update the slider accordingly
- [ ] update the slice number accordingly (upper left corner of the viewer window)
* down and up arrow keys
- [ ] jump to the next or previous brain within one project, respectively
- [ ] update the selected subject in the annotation table
* **TOOL BUTTONS**
* minus
- [ ] jumps to the previous slice within one brain
- [ ] updates the slider accordingly
- [ ] updates the slice number accordingly (upper left corner of the viewer window)
* plus
- [ ] jumps to the next slice within one brain
- [ ] updates the slider accordingly
- [ ] updates the slice number accordingly (upper left corner of the viewer window)
* slider
- [ ] updates slice view and slice number on the fly
* sag / cor / axi buttons
- [ ] switch view between the three orthogonal planes
* show tool
- [ ] when you click and drag in your browser window, this tool displays a cirlce at the position of your mouse click & drag as well as the user name in all browser windows connected to the same brain
* the numbers at the bottom of the tool panel
- [ ] change pencil size and eraser size accordingly
* pencil tool
- [ ] draws a line in the colour displayed in the color field
- [ ] in combination with bucket tool filles a complete area with the chosen colour (be sure to have closed the contour line ;) Otherwise, the undo button will be your friend ;)
- [ ] updates length and volume information (of what has been segmented) in the upper left corner of the viewer
* erase tool
- [ ] erases upon click drag from the annotation
- [ ] in combination with the bucket tool erases the complete area of the color where you click
* fill bucket tool
* in combination with pencil tool
- [ ] fills a complete area with the colour displayed in the colour field
* in combination with erase tool
- [ ] erases the complete area that is filled by the colour of where you click
* colour field
- [ ] displays the currently chosen colour to draw and fill
- [ ] on click opens the set of colours available within the chosen label set where a new colour can be selected upon click
* ruler tool
- [ ] measures the distance between start and end of your defined path
- [ ] points of mouse click appear and stay visible until you hit return key (this functionality is currently broken!) (you can click as many points as you wish to define the path you are interested in)
- [ ] on return key, BrainBox will print the distance into the chat field (the ruler tool seems to be currently broken!!!)
* adjust tool
- [ ] slide opacity of overlaid annotation from 0 to 100%
- [ ] increase or decrease brightness of the underlying MRI data
- [ ] increase or decrease the contrast of the underlying MRI data
* eyedropper tool
- [ ] updates the colour field in the tool panel
- [ ] displays/updates the region name in the upper left corner of the viewer
* undo tool
- [ ] undoes the user's actions in reverse chronological order and currently has the bug that it even undoes actions in slices you are currently not seeing! and there is currently no redo...
* save button
- [ ] saves the annotation of the data set into the data base
- [ ] displays a message that user needs to login in case they are not (CHECK!)
- [ ] display a message `Atlas saved Wed Oct 18 2017 12:49:12 GMT+0200 (CEST)`
<!-- Either or. Please replace `__` with appropriate data: -->
- [ ] I implemented tests for these changes OR
- [ ] These changes do not require tests because _____
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<!-- Again, many many thanks for your work! \ö/ -->
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