Grid enchancements

[neuroBazzi]

For the grid, the client asked for the following enhancements: 1) the relative size of the grid and its content in the 2D viewer gets larger and occupies large portion of the 2D viewer (now there is a lot of empty space around the grid); 2) The grid becomes bigger and ranges 2.5mm (or 2.6 in width) x 2mm (height), the slice will be at the center and have some empty space around it. The range on the y axis would be 2.5 mm, with the first/last numbers displayed -1.25 and 1.25, for the y axes the range is about 2 mm. The pitch of the ticks should be the same on both axes (0.1 mm ideally), we can display numbers every 0.4 or 0.5 mm as it works best as long as they're mirrored around the 0 (see below); 3) The numbers on the grid are mirrored, namely same values on the left and on the right of the 0 (same goes for above/below the 0). For example if the numbers on the right are 0.4, 0.8, 1.2, 2.4, the ones on the left will be the same (except negative); 4) It is hard to understand to which tick the number refers to, could we make the tick associated with the number a little longer or thicker or more obvious that it is the one associated with the number? 5) the 0 on the x axes seems a little off (I could be wrong); 6) The 0 of the z-Axis is in C8 caudal, not C8 rostral (they changed their mind); 7) Add the unit 'mm' on both axes, where it fits best; 8) The z-axis indicator which is now a number in the top right corner should have the label: Z-axis position (center in C8 Caudal): XX mm; (and maybe move it inside) 9) Possibility to toggle the grid on/off; 10) Bonus feature (add on to feature 9, it is not strictly required but a nice to have): the grid exists in three states 'off' (it's not there), 'frame' (it's there as we see it now, so a frame around the slide), or 'grid' (where the major lines of the grid -- so not all the lines at 1 mm pitch, but the ones associated with the numbers, so the ones at 0.4 or 0.5 mm pitch-- are overlaid on top of the slide). The toggle switch should be somewhere in the 2D viewer. this one might be hard to maybe tackle it last.

I know it does not sound like it, but they did really like the first version :-)

@zsinnema @afonsobspinto some of these tasks are probably more FE so I asked @vidhya-metacell to help us (she has hours for Salk in August). I am not sure what would be the best way to split up the work so I let you guys take a look at it, ideally this would go for sept 1 but there are some other important BE tasks for that date.

[zsinnema]

@neuroBazzi ad 1. the space on the left and right side of the grid can't be used because of the ratio of the grid. If we "expand" the x then the y should also "expand" but there is no room left above and below. we can expand a little bit more (reduce the margins). In order to see a "bigger" image move the panel to next to the 3D view panel, and do the same for the Electrophysiology panel. Then everything should show more "filled" up.

ad 2. parts of this task are unclear... do they mean they want fixed "sized" x and y axes, with fixed ticks?

ad 3. clear

ad 4. clear

ad 5. clear

ad 6. clear

ad 7. clear

ad 8. do I understand right that the full label should be exactly "Z-axis position (center in C8 Caudal): XX mm;" where XX will be dynamic and including the ";" at the end?

ad 9. clear, what's the default on or off?

ad 10. clear, so if we implement this the toggle should be: "off", "on", "lines"? and what will be the default?

[zsinnema]

@neuroBazzi only tasks 1 and 9 are 100% FE tasks, task 10 is 50-50 FE-BE the others are BE

[neuroBazzi]

@zsinnema thanks for the quick feedback. To answer your further questions: 1) makes sense, let's do what we can and try your suggestion; 2) yes to fixed size (or fixed range) and fixed values, the slices are all roughly the same size and will not change; 8) yes correct, except for the ";" at the end, we don't need it 9) default is on; 10) values would be: 'off', 'frame', 'grid' and the default would be grid (which is the equivalent of the on above)

ok thanks

[zsinnema]

@vidhya-metacell can you please do tasks 1 and 9

[zsinnema]

@neuroBazzi ad. 10 the values will be "off", "frame", "grid" where "grid" is the new feature. And not the equivalent of "on". I propose a radio group here with initial 2 values (task 9.) and then when task 10 is finished with 3 values. Even in 9. I would suggest to show "off" and "frame" where "frame" is the default. Then for 10 we only need to add the "grid" and make this one default

[neuroBazzi]

@zsinnema yes you're right, my bad. Ok the radio button solution with 'off' and 'frame' to start (and then adding 'grid') sounds good to me

[zsinnema]

@afonsobspinto yesterday I've done some testing and I think we need to change some things in the 2D viewer and image generators:

2D viewer:

• I suggest to use "plain" html img objects instead of drawing on the canvas, then the images can have css display: block or display: none. With position you can position the images on "top" of eachother
• instead of the css object: contain you could use margin: auto because we will need to show images with different "dimensions" (e.g. a grid with the same dimension on the x and y axes is a square and not the same as the atlas dimension)

Image generators:

• imo all the images should have the same margins except the grid because the grid "adds" something to the tiled images: a grid "around" the images. To have the grid in the same "unit" as the images the grid should have a different margin.
• the grid ticks on the x and y axes can be auto generated if you use plt.ylim() and plt.xlim()to set the min and max value on the axes
• I suggest to have the same x and y ax (-1.25 mm : 1.25 mm) and create a square image so that the units on x and y are the same
• may be it's also handy to make all other images a square (center the original image in a new square image)

hope this helps