I don't think there is a difference in meaning, only in usage.
This blog post details it:
“In contrast” and “by contrast” mean the same thing: the act of comparing in order to show differences.
The difference lies in the way the words are used.
“In contrast” is usually followed by “to” or “with” and requires a noun to follow it.
“By contrast” is usually followed or preceded by the subject of the sentence.
Examples:
In contrast to the diligent bee, the butterfly flies hither and yon with no apparent purpose.
In contrast with the chorus of birdsongs in my backyard, my front yard is serenaded by the sound of rumbling buses flying down the street.
By contrast, the Picasso is more vibrant and full of life.
The cats will often sleep the day away.
The dogs, by contrast, never settle down.
english.stackexchange.com/users/110/VonC
There is no difference in meaning.
But usually:
In contrast + to/with + noun By Contrast + subject of the sentence Note:
According to Longman Dictionary you can use "in contrast" + "(with/to)" Example For " in contrast ": The stock lost 60 cents a share, in contrast to last year , when it gained 21 cents.
Examples
For " by contrast ": The birth rate for older women has declined, but, by contrast , births to teenage mothers have increased.
english.stackexchange.com/users/3782/Manoochehr
The English make a distinction: in contrast is simply unlike; by contrast is unlike by comparison.
Economist March 27th 1993, p. 92.
english.stackexchange.com/users/32669/William solberg
Both 'in contrast' and 'by contrast' are prepositional expressions.
The usage is more versatile for 'in contrast' because it can be more naturally extended to include a substantive followed by 'to', to construct a more complex prepositional phrase with specific content, allowing one to use just one sentence instead of two (1) "
In contrast to bacterial infections diseases, viral infections cannot be treated with antibiotics.
" By contrast, 'By contrast' is more used as a simple prepositional expression in the sense of a modifying adverb, typically used to maintain the logical flow at the beginning of sentences: (2) "Bacterial infections can be treated with antibiotics.
By contrast/(In contrast), viral infections do not respond to to this class of drugs".
Note that (2) requires two sentences to say the say the same thing.
In the usage (2) one sees both 'in' and 'by contrast'.
However, editors at the leading British scientific journal NATURE, always correct 'in contrast' into 'by contrast' .
english.stackexchange.com/users/71664/S.E.H.
As a native English speaker, translator and proof reader, I prefer "in contrast", whereas "by contrast" always jars a little with me (I just came across it in a text I'm revising right now).
I can't explain why
and I don't know if there is a hard and fast rule (I doubt it),
but that's my two cents.
When in doubt, leave it out!
english.stackexchange.com/users/26810/Leni Nawocam
Can anyone explain the difference between  by contrast  and  in contrast ?
What is the difference between "by contrast" and "in contrast?"
english.stackexchange.com
<differences><prepositions>
english.stackexchange.com/questions/7642
english.stackexchange.com/users/3154/ALife
It is not clear that there is a difference meaning between "by contrast" and "in contrast". However, in usage, "by contrast" is usually followed by the subject of the sentence. There is no real difference in meaning.It depends on how the words are used.Personal preferences can dictate usage. There is a difference in English.They are prepositional expressions and usage can be tricky. But, if you are not sure don't use either. "In contrast", grammatically is more flexible.
It is not clear that there is a difference meaning between "by contrast" and "in contrast". However, in usage, "by contrast" is usually followed by the subject of the sentence. Some believe there is no real difference. “In contrast” is usually followed by “to” or “with” and "By contrast" is followed by the subject of the sentence. However, "In contrast" can be seen as more natural to some readers.
“In contrast” and “by contrast” mean the same thing: the act of comparing in order to show differences.    “In contrast” is usually followed by “to” or “with” and requires a noun to follow it.  “By contrast” is usually followed or preceded by the subject of the sentence.     It is generally considered that there is no difference in meaning between the two phrases by that they are used differently. "In contrast" is usually followed by "to" or "with", whereas "by contrast" is usually followed or proceded by the subject of the sentence. It is also possible that there is a slight distinction, with "in contrast" meaning "unlike" and "by contrast" meaning "unlike by comparison".
There is no difference in meaning. Use is different. It depends on how the words are used. There is a difference in English. They are prepositional expressions. "In contrast" grammatically is more flexible. Personal preferences can dictate usage. If you are not sure don't use either.
Some believe there is no real difference. “In contrast” is usually followed by “to” or “with” and "By contrast" is followed by the subject of the sentence. "In contrast" can be seen as more natural to some readers.
It is generally considered that there is no difference in meaning between "in contrast" and "by contrast". The difference may be in the way the phrases are used. "In contrast" is usually followed by "to" or "with". "By contrast" is usually followed or preceded by the subject of the sentence. The distinction is also said to be that "in contrast" is simply unlike whereas "by contrast" is unlike by comparison.