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Transparency over multiple pictureBoxes

I have an array of picture boxes that are arranged in a square. I want to put a larger, mostly transparent picture box over the top. But when I do it covers the other picture boxes and just draws the background of the form.
Is there a way to get it to have all the other picture boxes show where it is transparent?

Transparency in WinForms isn't great. Some controls have transparency support, others don't. Some controls can be subclassed to enable this (by calling Control.SetStyle() with the SupportsTransparency flag). I believe this can be done with PictureBox.
However, transparency in all WinForms controls works by having the transparent control call its parent control to draw the background before the child control draws. This means that you cannot have two sibling controls and expect transparency on one to show through to the other. Sorry!
All that said, it would be possible to code your own workaround to support this. It would involve subclassing PictureBox and clever coding in the OnPaint override to locate sibling controls and manually trigger painting of them into in-memory bitmaps. Lots of gotchas with this approach.
Try WPF!

Here's a tip to get the desired result:
Create multiple copies of your top image.
Add each copy to the Controls of each picture box it should cover.
Adjust location of each copy according to the offset of each picture box to be covered.
So you will see every copy of your big image covering each picture box as if they were a single image.

How can I create a transparent System.Windows.Forms.Panel on top of two other already existing Panels then draw a line on my transparent panel?

I'm writing a form in C# and have several panels. I need to draw a line between two of the panels. I've found online several ways to go about this, the most promising appears to be to create a third panel, make it transparent, place it on top of my original panels and draw the line here.
I'm not able to get the panel to be transparent, even if I set its BackColor and ForeColor properties to transparent (in code or in design view of VS).
Any ideas on how to make the panel itself transparent (or not Visible) but have the line I draw on it still visible on top of everything else?
Thanks in advance.

No, it's transparent. See this by giving the form's BackgroundImage a value. You'll see it through the transparent panel. Of course, that's not the kind of transparency you want, you want stacking effects to work. There is no direct support for that.
If you want layers to work then don't use controls. Use the Paint event to draw. Now there's no problem, if you want transparency then just don't paint. Draw a line across an image simply by drawing the image first. This is also the rendering model of WPF.

You can actually do this pretty easily as your own UserControl. Here's a code example:
Drawing on top of controls inside a panel (C# WinForms)
This is similar to what you were originally attempting to do, only instead of drawing a line on top of a transparent panel, this code creates an irregularly-shaped user control (which happens to be in the irregular shape of a line).

How to make any control shape irregular in c#

how to make any control of win application transparent. i want that i will assign a background image for the target control and will invoke a routine and that routine will create that control transparent in such a way that only image will visible. as a example suppose image has assign to picture box. the picture shape is not square rather irregular. if i can make picture box transparent then user will see the image only. basically i want to make a picture box or any control irregular shape. how to achieve it through code in c#.
thanks

In WPF, transparency is quasi for free. For the image-element, assign a png-image with an alpha mask and the image will be rendered with active transparency.
For controls with an solid background, you generally have to set the Background to a transparent Brush:
If you want to make a whole window partial transparent, you have to remove the border, set the window style to none, set the background brush to a transparent brush, and set the AllowsTransparency-property of the window to true.

there is one for ordinary winform at
http://www.youtube.com/watch?v=K_JzL4kzCoE

Animation Effects in WinForms/C#

I'm pasting an image from the game im building.
the matrix of empty cells you see are made of PictureBox[][].
I wan't whenever I drop a coin to one of the columns... I want it to go down but the purple stuff will hide the falling coin and the gray color you see wont hide it.
How do I make this effect?
please notice that in each PictureBox control I have set the BG Image as you can see

Don't do it like that.
Create custom control. In custom control, override Paint, and then draw COIN sprite first, then draw mask over it. Be sure that you use double-buffered painting here.
It will work like a charm, trust me!
And, since you are (I gueess) building 5-in-a-row game here, your custom control will be able to paint occupied slots as well.
By designing custom control, you'll be able to hide all the animation and graphics stuff away from your main form.

I don't think it is possible like that. Controls in WinForms cannot be transparent, that is the problem
I would think in three directions:
Forgetting about controls and
painting everything OnPaint event of
the form. It is not too complicated
(well it would be more complicated
to detect some mouse events like you
did now, as you wouldn't know which
graybox is hit, but rather just
mouse coordinates)
Experimenting with coin as a form
(forms can be transparent)
Possibly using WPF with same logic
you did, as controls can be
transparent there

Controls in Windows Forms can be transparent. You need to set the TransparencyKey of the Form to some color that you never plan on using (many people seem to love/hate Magenta for this), and then set the BackgroundColor of each PictureBox to the same color. The result should be a transparent PictureBox with its Image drawn over it. I'm pretty sure this won't work with the BackgroundImage property, mind you- just the Image property.
One potentially unwanted side effect of this method is that you'll be able to see whatever's behind your form (the desktop, other application windows, etc.) through the transparent places in the PictureBox.

Transparent PNG in PictureBox

I am trying to make simple app that allows one to compare image to transparent PNG templates, by dragging the template over picture. For this I need a way to create a PictureBox that will contain the PNG image and be transparent where the the png is transparent.
Everything works fine but the transparency part: When I load a PNG image to the PictureBox (background color is set to transparent) it shows the background color of the containing panel rather than the image that it hovers.
I searched but only found a way to make the PictureBox completely transparent.

It is difficult to make a control that is partially transparent.
What you should do is handle the lower PictureBox's Paint event (the one that does not need to be transparent), and draw the overlay image using e.Graphics.DrawImage(image, x, y). This will draw transparent and semi-transparent images correctly.
EDIT: In response to your comment, there's nothing wrong with calling the Invalidate method in the MouseMove event. However, you will notice some flickering. To solve the flickering, make a control that inherits PictureBox, and call SetStyle(ControlStyles.DoubleBuffered, true) in the constructor.

This works fine if you add the pictureBoxOnTop to the list of controls of the pictureBoxToBeHovered to be hovered.
pictureBoxToBeHovered.Controls.Add(pictureBoxOnTop);
pictureBoxOnTop.BackColor = Color.Transparent;
pictureBoxOnTop .Location = new Point(0,0) ;